All working as expected now thankyou.

I think the key change was setting the correct Z height

M208 X305 Y332 Z350 S0 ; 

now;

M208 X305 Y332 Z950 S0 ; 

Full Gcode;

950 ; Configuration file for Duet WiFi (firmware version 3)
; executed by the firmware on start-up
;
; generated by RepRapFirmware Configuration Tool v3.1.4 on Sat Sep 05 2020 23:57:30 GMT+0100 (British Summer Time)

; General preferences
M80					       	; Turns on the ATX power supply
G90                                            	; send absolute coordinates...
M83                                            	; ...but relative extruder moves
M550 P"BLV MGN Cube"                           	; set printer name
M669 K1                                        	; select CoreXY mode

; Network
M552 S1                                        	; enable network
M586 P0 S1                                     	; enable HTTP
M586 P1 S0                                     	; disable FTP
M586 P2 S0                                     	; disable Telnet

; Drives
M569 P0 S0                                     	; physical drive 0 goes backwards
M569 P1 S1                                     	; physical drive 1 goes forwards
M569 P2 S1                                     	; physical drive 2 goes forwards
M569 P3 S0                                     	; physical drive 3 goes backwards
M584 X0 Y1 Z2 E3                               	; set drive mapping
M350 X16 Y16 Z16 E16 I1                        	; configure microstepping with interpolation
M92 X200.00 Y200.00 Z800.00 E415.5             	; set steps per mm
M566 X600.00 Y600.00 Z24.00 E300.00            	; set maximum instantaneous speed changes (mm/min)
M203 X20000.00 Y20000.00 Z600.00 E2000.00      	; set maximum speeds (mm/min)
M201 X3000.00 Y3000.00 Z100.00 E5000.00        	; set accelerations (mm/s^2)
M906 X1500 Y1500 Z1500 E1100 I30               	; set motor currents (mA) and motor idle factor in per cent
M84 S30                                        	; Set idle timeout

; Pressure advance
; M572 D0 S0.05	

; Axis Limits
M208 X-23 Y0 Z0 S1                            	; set axis minima
M208 X305 Y332 Z950 S0                        	; set axis maxima

; Endstops
M564 H0					       	; allow jog without homing
M574 X1 S1 P"xstop"                            	;
M574 Y2 S1 P"ystop"                            	;
M574 Z1 S1 P"zstop"                            	; configure Z-probe endstop for low end on Z

; Z-Probe
M558 P1 H5 C"^zprobe.in" H5 F250 T9000 R0.5	; set Z probe type to switch and the dive height + speeds
G31 P500 X-2 Y-16.4 Z1.40                      	; set Z probe trigger value, offset and trigger height
M557 X10:292 Y5:300 P5                       	; define mesh grid

; Heaters
M308 S0 P"bedtemp" Y"thermistor"T100000 B3950 C0 R4700 A"Bed Temp"  	; configure sensor 0 as thermistor on pin bedtemp
M950 H0 C"bedheat" T0                          				; create bed heater output on bedheat and map it to sensor 0
M140 H0                                        				; map heated bed to heater 0
M143 H0 S100                                   				; set temperature limit for heater 0 to 100C
M307 H0 A466.3 C1262.5 D12.8 S1.00 V24.0 B0    				; Set PID for heated bed values
M308 S1 P"e0temp" Y"thermistor" T100000 B3950 C0 R4700 A"Hotend Temp"   ; configure sensor 1 as thermistor on pin e0temp
M950 H1 C"e0heat" T1                           				; create nozzle heater output on e0heat and map it to sensor 1
M143 H1 S260                              				; set temperature limit for heater 1
M307 H1 A340.0 C140.0 D5.5 S1.00 V24.0 B0     				; Set PID for hotend values

; Fans
M950 F0 C"fan0" Q500                           	; create fan 0 on pin fan0 and set its frequency
M106 P0 S0 H-1                                 	; set fan 0 value. Thermostatic control is turned off
M950 F1 C"fan1" Q500                           	; create fan 1 on pin fan1 and set its frequency
M106 P1 S1 H1 T45                              	; set fan 1 value. Thermostatic control is turned on

; Tools
M563 P0 D0 H1 F0                               	; define tool 0
G10 P0 X0 Y0 Z0                                	; set tool 0 axis offsets
G10 P0 R0 S0                                   	; set initial tool 0 active and standby temperatures to 0C

@Phaedrux said in problems with pressure advance calibration:

retract on layer change

Thank you. Yes I have retract on layer change enabled

I've changed the z values you suggested and set the slicer to start the pressure advance at 0.035 in increments to 0.055. Printing now

@phaedrux

update - after making a few changes the hotend is now heating without the error.

The all metal throat is secured by two grub screws to the body/heatsink. Although properly secured, I think the throat was heating up, expanding slightly and making better contact with the heatsink, causing it to dump heat a bit quicker and triggering the error.
I've added some thermal compound to the throat/heatsink, re-tuned and can now heat from cold without any issues.

@phaedrux

update - after making a few changes the hotend is now heating without the error.

The all metal throat is secured by two grub screws to the body/heatsink. Although properly secured, I think the throat was heating up, expanding slightly and making better contact with the heatsink, causing it to dump heat a bit quicker and triggering the error.
I've added some thermal compound to the throat/heatsink, re-tuned and can now heat from cold without any issues.

@nick9one1 my bad.. just needed to drop "[output_filepath]".

All working, thanks @zapta

@zapta
Perfect thanks I've got it working from the command line with your code.

Now I just need to work out why it wont run in superslicer..

If create a .gcode file and run this from cmd, it works..

C:\Users\mumby\AppData\Local\Programs\Python\Python39\python.exe "C:\Users\mumby\OneDrive\Desktop\duet3d_automesh.py" "C:\Users\mumby\OneDrive\Desktop\box.gcode"

but this doesnt work from the prusaslicer..

C:\Users\mumby\AppData\Local\Programs\Python\Python39\python.exe "C:\Users\mumby\OneDrive\Desktop\duet3d_automesh.py" "[output_filepath]" 

I found a nice that reduces the probe area based on what youre printing script originally written by CCS86 and modified by @Luke-sLaboratory, then later modified by @zapta Unfortunately zaptas github link no longer works

Nevertheless, using luke's version, I cant get it to work.

I've sliced a simple cube in superslicer and have been running it from the command line;

python3 "C:\Program Files\SuperSlicer\meshgrid.py" "C:\Users\mumby\OneDrive\Desktop\Shape-Box.gcode"

Starting Mesh Calculations
Bounds are: {'X': {'min': 137, 'max': 181}, 'Y': {'min': 117, 'max': 161}}
Traceback (most recent call last):
  File "C:\Program Files\SuperSlicer\meshgrid.py", line 206, in <module>
    main(fname = sys.argv[1])
  File "C:\Program Files\SuperSlicer\meshgrid.py", line 67, in main
    linesNew = calcBed(lines)
  File "C:\Program Files\SuperSlicer\meshgrid.py", line 86, in calcBed
    bed = findBed()
  File "C:\Program Files\SuperSlicer\meshgrid.py", line 119, in findBed
    maxXY = bedCorners.split(',')[2].split('x')
AttributeError: 'NoneType' object has no attribute 'split'

the gcode im trying to run it against;
https://github.com/nick9one1/superslicer_automesh/blob/main/Shape-Box.gcode

the script;
https://github.com/nick9one1/superslicer_automesh/blob/main/meshgrid.py

Sounds similar to my issue
https://forum.duet3d.com/topic/22274/strange-message-when-pid-tuning/12

3mm-4mm gap between heat block and cold side.

There's quite a lot of thermal mass with the complete extruder assembly being 100% metal. My initial thoughts were this was the reason for the error. But the pid tuning should take account of this? (tuning was done from cold).

sure..

A couple of stock images, then three of my setup.
It way be worth mentioning the whole assembly is aluminium.. The block, gears, extruder housing, tensioning arm.
Its fairly similar to the E3d Hermera, although smaller and lighter.

I had to add M501 at the end of config.g (as I dont usually use config-override.g)

; Configuration file for Duet WiFi (firmware version 3)
; executed by the firmware on start-up
;
; generated by RepRapFirmware Configuration Tool v3.1.4 on Sat Sep 05 2020 23:57:30 GMT+0100 (British Summer Time)

; General preferences
M80					       	; Turns on the ATX power supply
G90                                            	; send absolute coordinates...
M83                                            	; ...but relative extruder moves
M550 P"BLV MGN Cube"                           	; set printer name
M669 K1                                        	; select CoreXY mode

; Network
M552 S1                                        	; enable network
M587 S"your_wifi_name" P"your_password"        	; Configure access point. You can delete this line once connected
M586 P0 S1                                     	; enable HTTP
M586 P1 S0                                     	; disable FTP
M586 P2 S0                                     	; disable Telnet

; Drives
M569 P0 S0                                     	; physical drive 0 goes backwards
M569 P1 S1                                     	; physical drive 1 goes forwards
M569 P2 S1                                     	; physical drive 2 goes forwards
M569 P3 S0                                     	; physical drive 3 goes backwards
M584 X0 Y1 Z2 E3                               	; set drive mapping
M350 X16 Y16 Z16 E16 I1                        	; configure microstepping with interpolation
M92 X200.00 Y200.00 Z3200.00 E932.00            ; set steps per mm
M566 X820.00 Y820.00 Z70.00 E500.00             ; set maximum instantaneous speed changes (mm/min)
M203 X20000.00 Y20000.00 Z500.00 E2000.00      	; set maximum speeds (mm/min)
M201 X3000.00 Y3000.00 Z150.00 E5000.00        	; set accelerations (mm/s^2)
M906 X1100 Y1100 Z1100 E800 I30               	; set motor currents (mA) and motor idle factor in per cent
M84 S30                                        	; Set idle timeout

; Pressure advance
M572 D0 S0.1

; Axis Limits
M208 X-30 Y0 Z0 S1                            	; set axis minima
M208 X305 Y329 Z950 S0                        	; set axis maxima

; Endstops
M564 H0					       					; allow jog without homing
M574 X1 S1 P"xstop"                            	;
M574 Y2 S1 P"ystop"                            	;
M574 Z1 S1 P"zstop"                            	; configure Z-probe endstop for low end on Z

; Z-Probe
M558 P1 H5 C"^zprobe.in" H5 F250 T9000 R0.5 T7200	; set Z probe type to switch and the dive height + speeds
G31 P500 X0 Y25 Z1.97                      			; set Z probe trigger value, offset and trigger height
M557 X10:280 Y25:278 P5                      		; define mesh grid

; Heaters
M308 S0 P"bedtemp" Y"thermistor" T100000 B3950 C0 A"Bed Temp" 				; configure sensor 0 as thermistor on pin bedtemp
M950 H0 C"bedheat" T0                          								; create bed heater output on bedheat and map it to sensor 0
M140 H0                                        								; map heated bed to heater 0
M143 H0 S100                                   								; set temperature limit for heater 0 to 100C
;M307 H0 A340.0 C445.4 D27.6 S1.00 V23.9 B0									; Set PID for heated bed values
M307 H0 R0.278 C1408.5 D27.03 S1.00											; Set PID for bed values
M308 S1 P"e0temp" Y"thermistor" T100000 B3950 A"Hotend Temp"  				; configure sensor 1 as thermistor on pin e0temp
M950 H1 C"e0heat" T1                           								; create nozzle heater output on e0heat and map it to sensor 1
M143 H1 S265                              									; set temperature limit for heater 1
M307 H1 R3.349 C228.7:133.4 D7.83 S1.00 V23.9								; Set PID for hotend values
		
; Fans
M950 F0 C"Fan2" Q50                        	; create fan 0 on pin 2 and set its frequency
M106 P0 S0 H-1 X204                             ; set fan 0 value. Thermostatic control is turned off
;M950 F0 C"Fan0" Q100                           ; create fan 2 on pin fan2 and set its frequency
;M106 P0 S1 H1 T45                              ; set fan 2 value. Thermostatic control is turned on

; Tools
M563 P0 D0 H1 F0                               	; define tool 0
G10 P0 X0 Y0 Z0                                	; set tool 0 axis offsets
G10 P0 R0 S0                                   	; set initial tool 0 active and standby temperatures to 0C

; Screen
M575 P1 B57600 S1


M501

and config-override.g

; config-override.g file generated in response to M500 at 2021-03-21 01:19
; This is a system-generated file - do not edit
; Heater model parameters
M307 H0 R0.278 C1408.500:1408.500 D27.03 S1.00 V0.0 B1
M307 H1 R3.445 C219.932:130.532 D7.80 S1.00 V23.9 B0
; Workplace coordinates
G10 L2 P1 X0.00 Y0.00 Z0.00
G10 L2 P2 X0.00 Y0.00 Z0.00
G10 L2 P3 X0.00 Y0.00 Z0.00
G10 L2 P4 X0.00 Y0.00 Z0.00
G10 L2 P5 X0.00 Y0.00 Z0.00
G10 L2 P6 X0.00 Y0.00 Z0.00
G10 L2 P7 X0.00 Y0.00 Z0.00
G10 L2 P8 X0.00 Y0.00 Z0.00
G10 L2 P9 X0.00 Y0.00 Z0.00
M486 S-1

Unfortunately I get exactly the same..

Thanks. I'll try that

I've changed M308 to reflect more 'default' settings, re-tuned, but still get the same error...

M308 S1 P"e0temp" Y"thermistor" T100000 B3950 A"Hotend Temp"