@dc42 Sorry, I forgot post my config file.

; General preferences
G90                                            ; send absolute coordinates...
M83                                            ; ...but relative extruder moves
M550 P"duet"                                 ; set printer name
M669 K1                                        ; select CoreXY mode

; Network
;M552 P0.0.0.0 S1                               ; enable network and acquire dynamic address via DHCP
;M586 P0 S1                                     ; enable HTTP
;M586 P1 S0                                     ; disable FTP
;M586 P2 S0                                     ; disable Telnet

; Drives -
M569 P0.0 S1                                   ; physical drive 0.0 goes forwards
M569 P0.1 S1                                   ; physical drive 0.1 goes forwards
M569 P0.2 S0                                   ; physical drive 0.2 goes backwards
M569 P0.3 S0                                   ; physical drive 0.3 goes backwards
M569 P0.4 S0                                   ; physical drive 0.4 goes backwards
M569 P1.0 S0                                 ; physical drive 1.0 goes backwards
M584 X0.0 Y0.1 Z0.2:0.3:0.4 E1.0             ; set drive mapping
M350 X32 Y32 Z64 E16 I1                        ; configure microstepping with interpolation
M92 X160.00 Y160.00 Z1600.00 E409.00           ; set steps per mm

; Calculated values from https://www.3dblog.cz/nastaveni/akcelerace-jerk-a-junction-deviation/
M201 X3200.00 Y3200.00 Z100.00 E2000.00        ; set accelerations (mm/s^2)
M203 X12000.00 Y12000.00 Z300.00 E10000.00        ; set maximum speeds (mm/min)
M204 P1400 										; Set printing acceleration
M205 X12.00 Y12.00 Z12.00 E12.00            ; set maximum instantaneous speed changes (mm/min)

M906 X1773 Y1773 Z1773 E940 I30               ; set motor currents (mA) and motor idle factor in per cent
M84 S30                                        ; Set idle timeout

; Axis Limits
M208 X-4:270 Y-4:270 Z0:270                               ; set axis minima/maxima

; Endstops
M574 X1 S1 P"!1.io1.in"                       ; configure sensorless endstop for low end on X
M574 Y1 S1 P"!io1.in"                         ; configure sensorless endstop for low end on Y
M574 Z1 S2                                     ; configure Z-probe endstop for low end on Z

; Z-Probe
M950 S0 C"1.io0.out"                         ; create servo pin 0 for BLTouch
M558 P9 C"^1.io0.in" H1.5 F240 T12000           ; set Z probe type to bltouch and the dive height + speeds
G31 P1000 X36 Y-44 Z4.50                            ; set Z probe trigger value, offset and trigger height
M557 X32:270 Y0:226 P8                       ; define mesh grid

; Heaters
M308 S0 P"temp0" Y"thermistor" T90000 B4000 A"Bed" D600 ; configure sensor 0 as thermistor on pin temp0
M950 H0 C"out1" T0                             ; create bed heater output on out0 and map it to sensor 0
M140 H0                                        ; map heated bed to heater 0
M143 H0 S130                                   ; set temperature limit for heater 0 to 130C

M308 S1 P"1.temp0" Y"pt1000" A"Nozzle"; configure sensor 1 as PT1000 on pin 1.temp0
M950 H1 C"1.out0" T1                           ; create nozzle heater output on 1.out0 and map it to sensor 1
;M950 H1 C"out0" T1                           ; (TUNING PURPOSES - M303 only) create nozzle heater output on out0 and map it to sensor 1
M143 H1 S285                                   ; set temperature limit for heater 1

; Fan
M950 F0 C"!1.out1+^out1.tach" Q1000                            ; create fan 0 on pin 1.out1 and set its frequency (Blower)
M106 P0 S0 H-1 B0.2                            ; set fan 0 value. Thermostatic control is turned off
M950 F1 C"1.out2+^out2.tach"                            ; create fan 1 on pin 1.out2 and set its frequency (Heatsink)
M106 P1 S1 H1 T45                              ; set fan 1 value. Thermostatic control is turned on

; Tools
M563 P0 D0 H1 F0 S"Hemera"                               ; 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

; Custom settings are not defined

; Miscellaneous
M575 P1 S1 B57600                              ; enable support for PanelDue

; Resetting Z-probe
M280 P0 S160 ; Alarm Release and Push-Pin UP
M280 P0 S90 ; Send PWM channel 0 the S90 (angle) command

;M290 M290 R0 S-0.040							; Baby Z-offset

M572 D0 S0.025									; Configure pressure advance

;M564 H0											; allow movement of axes that have not been homed

M501											; Set the active parameters to those stored in sys/config-override.g on the SD card.

@Meltex @dc42 My issue is propably different. When it fails, toolboard is always keeping correct temperature at nozzle. It normally continues printing, toolboard is only reporting wrong temperature to Duet motherboard.
When I reset toolboard (unplug/plug power to whole printer), after startup it shows last correct temperature, few degrees below last defined temperature (hotend is cooled few degrees during restart).
So, PT1000 sensor is all time (even when toolboard reports fault to Duet board and 2000 °C) reporting correct temperature to the toolboard.

@dc42 It always happens after few hours of printing. It never happens at the beginning of printing.

@dc42 And hello again... Problem with 2000 °C persists also in RC1 release...

I don't know if that could be an issue, but I'm using PT1000 sensor instead of thermistor...

Diagnostics for board 1:
Duet TOOL1LC firmware version 3.2-RC1 (2020-12-19)
Bootloader ID: not available
Never used RAM 3960, free system stack 38 words
HEAT 86 CanAsync 89 CanRecv 83 TMC 54 MAIN 219 AIN 64
Last reset 03:17:23 ago, cause: power up
Last software reset at 2020-11-22 15:02, reason: HardFault, available RAM 4168, slot 0
Software reset code 0x0060 ICSR 0x00000003 SP 0x200011c8 Task  Freestk 4294967295 ok
Stack: 20001018 20001304 0000000f 00000001 20000928 000172cd 00018250 01000000 00077dfa 00077ef4 20001218 200032d0 00000020 00017a61 20004660 00000000 20001300 00008895 00077dfa 20004670 00077ef4 42651000 a5a5a5a5 a5a5a5a5 a5a5a5a5 a5a5a5a5 a5a5a5a5
Driver 0: position 7455393, 409.0 steps/mm, standstill, SG min/max 0/112, read errors 0, write errors 0, ifcnt 16, reads 23696, writes 16, timeouts 0, DMA errors 0
Moves scheduled 218054, completed 218054, in progress 0, hiccups 0
No step interrupt scheduled
VIN: 24.2V
MCU temperature: min 36.8C, current 51.7C, max 62.4C
Ticks since heat task active 198, ADC conversions started 11796908, completed 11796907, timed out 0
Last sensors broadcast 0x00000002 found 1 202 ticks ago, loop time 0
CAN messages queued 142406, send timeouts 0, received 324917, lost 0, free buffers 36

My setup is this:

M308 S1 P"1.temp0" Y"pt1000" A"Nozzle"; configure sensor 1 as PT1000 on pin 1.temp0
M950 H1 C"1.out0" T1                           ; create nozzle heater output on 1.out0 and map it to sensor 1
M143 H1 S285                                   ; set temperature limit for heater 1

@dc42 Hi again. Problem with 2000 °C is back.
It's keeping same temperature, but it reports nonsense. This is M122 output:

Diagnostics for board 1:
Duet TOOL1LC firmware version 3.2-beta4.1+1 (2020-12-12)
Bootloader ID: not available
Never used RAM 3960, free system stack 36 words
HEAT 86 CanAsync 89 CanRecv 83 TMC 54 MAIN 209 AIN 64
Last reset 04:39:13 ago, cause: software
Last software reset at 2020-11-22 15:02, reason: HardFault, available RAM 4168, slot 0
Software reset code 0x0060 ICSR 0x00000003 SP 0x200011c8 Task 
Stack: 20001018 20001304 0000000f 00000001 20000928 000172cd 00018250 01000000 00077dfa 00077ef4 20001218 200032d0 00000020 00017a61 20004660 00000000 20001300 00008895 00077dfa 20004670 00077ef4 42651000 a5a5a5a5 a5a5a5a5 a5a5a5a5 a5a5a5a5 a5a5a5a5
Driver 0: position 7738615, 409.0 steps/mm, standstill, SG min/max 0/112, read errors 0, write errors 1, ifcnt 42, reads 53596, writes 14, timeouts 0, DMA errors 0
Moves scheduled 219075, completed 219075, in progress 0, hiccups 0
No step interrupt scheduled
VIN: 24.2V
MCU temperature: min 38.4C, current 54.5C, max 57.9C
Ticks since heat task active 151, ADC conversions started 16686702, completed 16686701, timed out 0
Last sensors broadcast 0x00000002 found 1 155 ticks ago, loop time 0
CAN messages queued 201492, send timeouts 0, received 370230, lost 0, free buffers 36

@dc42 I have same problem. After few hours of printing the extruder heater goes offline, temperature goes to 2000 °C (I'm using PT1000)

Updated to latest 3.2-beta4.1 and problem remains. It keeps printing so I guess it's still keeping 220 °C, but to CAN bus it reports offline status.
M122 on Toolboard says:

Diagnostics for board 1:
Duet TOOL1LC firmware version 3.2-beta4.1 (2020-12-03)
Bootloader ID: not available
Never used RAM 4120, free system stack 36 words
HEAT 46 CanAsync 89 CanRecv 83 TMC 54 MAIN 216 AIN 64
Last reset 11:35:12 ago, cause: software
Last software reset at 2020-11-22 15:02, reason: HardFault, available RAM 4168, slot 0
Software reset code 0x0060 ICSR 0x00000003 SP 0x200011c8 Task 
Stack: 20001018 20001304 0000000f 00000001 20000928 000172cd 00018250 01000000 00077dfa 00077ef4 20001218 200032d0 00000020 00017a61 20004660 00000000 20001300 00008895 00077dfa 20004670 00077ef4 42651000 a5a5a5a5 a5a5a5a5 a5a5a5a5 a5a5a5a5 a5a5a5a5
Driver 0: position 11794334, 409.0 steps/mm, standstill, SG min/max 0/112, read errors 0, write errors 1, ifcnt 35, reads 15910, writes 16, timeouts 0, DMA errors 0
Moves scheduled 562468, completed 562468, in progress 0, hiccups 0
No step interrupt scheduled
VIN: 24.2V
MCU temperature: min 39.2C, current 41.7C, max 51.2C
Ticks since heat task active 43, ADC conversions started 41546663, completed 41546662, timed out 0
Last sensors broadcast 0x00000002 found 1 47 ticks ago, loop time 0
CAN messages queued 501025, send timeouts 0, received 938189, lost 0, free buffers 36

Any thoughts? Can I contribute with more debug infos to solve this?

Thank you for advice! In standalone setup I was able to upgrade it.

I have Duet 3 SBC + Toolboard. Upgraded from 3.2-b3.
I did:
apt update
apt upgrade

then reboot.

Started normally, then I did M997 B1 (current address of my toolboard). After that, it failed with msg "Error: Firmware file Duet3Firmware_TOOL1LC.bin not found" and it repeats this msg every 7 secs. Both fans are running at 100% power constantly.
File Duet3Firmware_TOOL1LC.bin is located in sys directory, I can download it in browser, I tried upload it again. No success.
It seems Toolboard disappeared from CAN bus, it doesn't respond to m115 b1 neither m115 b121.

I tried reset Toolboard to factory settings (pushing both triggers on Toolboard during startup) with no success.
Any idea how to wake up and upgrade Toolboard in this scenario?

@bearer Thanks man!

Does anyone has successfully connected Duet 3 board and Toolboard?
See the picture (original from Duet). It says (under black wire) RJ11 Pin 3 -> JST Pin 4 and (above red wire) RJ11 Pin 4 -> JST Pin 3. But picture (red and black wire) shows connection RJ11 Pin 3 -> JST Pin 3 and RJ11 Pin 4 -> JST Pin 4.
Does anyone know if text descripton is correct or picture is correct?