After extending and moving the y-axis endstop connector from the duex to the duet I haven't had any more disconnects and everything seems to be working correctly.

Thank you so much.

@droftarts
I'll double check the connectors for any shorts tonight.
Yes the disconnects happen on both the x and y axis endstops, it doesn't seem to happen more often on one or the other.

These are the endstops I'm using. I had them wired in the same way on the previous version of my printer and didn't have any issues.

Currently I'm using the new SD card that came with the new board. I'll try a freshly formatted one too.

@droftarts
I have tried both a fixed ip address and one assigned by the router and it hasn't helped.
I have tried connecting on my desktop (windows 10), macbook pro, ipad, and iphone and the same problem happens on all these devices

@dc42
Yes the y-axis endstop is connected to the duex5. Both the x-axis endstop and probe are connected to the duet.

@droftarts
This is my config file:

; Executed by the firmware on start-up
; Last updated June 8/2020

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

; Network
M551 P"mike17670" ; set password
M552 S1 ; enable networking
M586 P0 S1 ; enable HTTP
M586 P1 S0 ; disable FTP
M586 P2 S0 ; disable Telnet

; Drives
M584 X9 Y5 Z6:7:8 E3:4 ; Drive mapping, x=drive9, y=drive5, z=drive6+7+8, e=drive3+4
M569 P9 S0 ; physical drive 9 goes forwards
M569 P5 S0 ; physical drive 5 goes forwards
M569 P6 S0 ; physical drive 6 goes forwards (front right z motor)
M569 P7 S0 ; physical drive 7 goes forwards (rear right z motor)
M569 P8 S0 ; physical drive 8 goes forwards (center left z motor)
M569 P3 S1 ; physical drive 3 goes forwards
M569 P4 S1 ; physical drive 4 goes forwards
M350 X16 Y16 Z8 E16:16 I0 ; 1/16 microstepping for all motors, and enable microstepping interpolation up to 1/256
M92 X80.00 Y80.00 Z400.00:400.00:400.00 E420.00:420.00 ; set steps per mm
M566 X900.00 Y900.00 Z12.00:12.00:12.00 E120.00:120.00 ; set maximum instantaneous speed changes (mm/min)
M203 X6000.00 Y6000.00 Z180.00:180.00:180.00 E1200.00:1200.00 ; set maximum speeds (mm/min)
M201 X500.00 Y500.00 Z20.00:20.00:20.00 E250.00:250.00 ; set accelerations (mm/s^2)
M906 X800 Y800 Z1400:1400:1400 E800:800 I30 ; set motor currents (mA) and motor idle factor in per cent
M84 S30 ; Set idle timeout

; Axis Limits
M208 X0 Y0 Z0 S1 ; set minimums for each axis
M208 X400 Y400 Z400 S0 ; set maximums for each axis
M671 X335:335:-35 Y10.5:340.5:175.5 S1 ; set leadscrew locations for auto bed leveling and max correction in mm (front right, rear right, center left leadscrews)

; Endstops
M574 X2 S1 P"!e1stop" ; set x endstp location at max of axis, active low endstop, mapped to e1stop on duet wifi
M574 Y2 P"nul" ; free up y endstop
M574 Y2 S1 P"!duex.e6stop" ; set y endstop location at max of axis, active low endstop, mapped to e6stop on duex5
M574 Z1 S2 ; set z axis enstop at min of axis and controlled by probe

; Z-Probe
M558 P1 C"zprobe.in" H5 F120 T6000 ; set Z probe type to unmodulated/smart IR probe, connected to zprobe, dive height, feed rate, and travel speed between points
G31 P500 X0 Y0 Z2.5 ; set Z probe trigger value, XY offset and trigger height
M557 X15:215 Y15:195 S20 ; mesh grid, XY max/min values, and probe point spacing

; Heaters
M308 S0 P"bedtemp" Y"thermistor" T100000 B4138 R4700 ; define thermistor 0, set to bedtemp pins, thermistor type, and thermistor constants (bed thermistor)
M308 S1 P"e0temp" Y"thermistor" T100000 B4725 C7.06E-8 R4700 ; define thermistor 1, set to e0temp pins, thermistor type, and thermistor constants (extruder 0 thermistor)
M308 S2 P"e1temp" Y"thermistor" T100000 B4725 C7.06E-8 R4700 ; define thermistor 2, set to e1temp pins, thermistor type, and thermistor constants (extruder 1 thermistor)
M950 H0 C"bedheat" T0 ; define heater 0, set to bedheat pins, assign temperature sensor 0 to it (bed heater)
M950 H1 C"e0heat" T1 ; define heater 1, set to e0heat pins, assign temperature sensor 1 to it (extruder 0 heater)
M950 H2 C"e1heat" T2 ; define heater 2, set to e1heat pins, assign temperature sensor 2 to it (extruder 1 heater)
M140 H0 ; assign heater 0 as the bed heater
M307 H0 A208.8 C572.6 D1.0 V24.4 B0 S1.00 ; set PID calibration constants for heater 0 calibrated at 100 deg C, disable bang-bang mode for heater 0, set pwm limit to 1.00
M307 H1 A567.6 C228.7 D4.5 V24.4 ; set PID calibration constants for heater 1 calibrated at 250 deg C
M307 H2 A555.1 C244.4 D5.0 V24.4 ; set PID calibration constants for heater 2 calibrated at 250 deg C
M143 H0 S120 ; set temperature limit for heater 0 to 120 dec C
M143 H1 S280 ; set temperature limit for heater 1 to 280 deg C
M143 H2 S280 ; set temperature limit for heater 2 to 280 deg C

; Fans
M106 P0 S0 I0 F500 H-1 ; set fan number, fan speed, normal mode, PWM frequency, thermostatic mode off
M106 P1 S1 I0 F500 H1:2 T45 ; set fan number, fan speed, normal mode, PWM frequenct, thermostatic mode on for heaters 1 and 2

; Tools
M563 P0 D0 H1 F0 ; define tool 0, extruder drive, heater, and fan
G10 P0 X0 Y0 Z0 ; set tool 0 axis offsets
G10 P0 R0 S0 ; set initial tool 0 active and standby temperatures to 0C
M563 P1 D1 H2 F0 ; define tool 1, extruder drive, heater, and fan
G10 P1 X18 Y0 Z0 ; set tool 1 axis offsets
G10 P1 R0 S0 ; set initial tool 1 active and standby temperatures to 0C
M572 D0:1 S0 ; pressure advance for tools 0 and 1, amount of pressure advance (in seconds)

I have bought a brand new duet 2 ethernet board and am still having the same problems. Was hoping using an ethernet board would help.
I updated the new board to firmware 3.1.1 and this is my results for M112 immediately after it reconnects

M122
=== Diagnostics ===
RepRapFirmware for Duet 2 WiFi/Ethernet version 3.1.1 running on Duet Ethernet 1.02 or later + DueX5
Board ID: 08DLM-996RU-N8PS4-7JKD2-3S06T-9ABRN
Used output buffers: 3 of 24 (12 max)
=== RTOS ===
Static ram: 27980
Dynamic ram: 94104 of which 60 recycled
Exception stack ram used: 208
Never used ram: 8720
Tasks: NETWORK(ready,384) HEAT(blocked,1224) DUEX(suspended,160) MAIN(running,1824) IDLE(ready,80)
Owned mutexes:
=== Platform ===
Last reset 00:00:21 ago, cause: software
Last software reset at 2020-06-08 21:30, reason: Stuck in spin loop, spinning module Move, available RAM 8264 bytes (slot 1)
Software reset code 0x4084 HFSR 0x00000000 CFSR 0x00000000 ICSR 0x0041f80f BFAR 0xe000ed38 SP 0x200042e4 Task IDLE
Stack: 00454cdd 0045570c 61000000 a5a5a5a5 00454cdd a5a5a5a5 20004308 200041f8 00000002 2000512c 000124b9
Error status: 0
MCU temperature: min 30.2, current 30.9, max 31.1
Supply voltage: min 24.1, current 24.1, max 24.2, under voltage events: 0, over voltage events: 0, power good: yes
Driver 0: standstill, SG min/max not available
Driver 1: standstill, SG min/max not available
Driver 2: standstill, SG min/max not available
Driver 3: standstill, SG min/max not available
Driver 4: standstill, SG min/max not available
Driver 5: standstill, SG min/max not available
Driver 6: standstill, SG min/max not available
Driver 7: standstill, SG min/max not available
Driver 8: standstill, SG min/max not available
Driver 9: standstill, SG min/max not available
Date/time: 2020-06-08 21:31:20
Cache data hit count 39924084
Slowest loop: 5.22ms; fastest: 0.13ms
I2C nak errors 0, send timeouts 0, receive timeouts 0, finishTimeouts 0, resets 0
=== Storage ===
Free file entries: 10
SD card 0 detected, interface speed: 20.0MBytes/sec
SD card longest read time 3.2ms, write time 0.0ms, max retries 0
=== Move ===
Hiccups: 0(0), FreeDm: 169, MinFreeDm: 169, MaxWait: 0ms
Bed compensation in use: none, comp offset 0.000
=== MainDDARing ===
Scheduled moves: 0, completed moves: 0, StepErrors: 0, LaErrors: 0, Underruns: 0, 0 CDDA state: -1
=== AuxDDARing ===
Scheduled moves: 0, completed moves: 0, StepErrors: 0, LaErrors: 0, Underruns: 0, 0 CDDA state: -1
=== Heat ===
Bed heaters = 0 -1 -1 -1, chamberHeaters = -1 -1 -1 -1
=== GCodes ===
Segments left: 0
Movement lock held by null
HTTP is idle in state(s) 0
Telnet is idle in state(s) 0
File is idle in state(s) 0
USB is idle in state(s) 0
Aux is idle in state(s) 0
Trigger is idle in state(s) 0
Queue is idle in state(s) 0
Daemon is idle in state(s) 0
Autopause is idle in state(s) 0
Code queue is empty.
=== Network ===
Slowest loop: 8.15ms; fastest: 0.02ms
Responder states: HTTP(0) HTTP(0) HTTP(0) HTTP(0) FTP(0) Telnet(0), 0 sessions
HTTP sessions: 1 of 8
Interface state active, link 100Mbps full duplex
=== DueX ===
Read count 1, 2.76 reads/min

@Chriss any luck with determining what could be causing your disconnect issues?

I still haven't been able to find a solution for mine

After updating to the official 3.1.1 it seems to disconnect less randomly and seems to occur most often after an endstop is triggered while homing.

I installed the official 3.1.1 and am still having the same issues.

This is my results from M122 immediately after the board reconnects

M122
=== Diagnostics ===
RepRapFirmware for Duet 2 WiFi/Ethernet version 3.1.1 running on Duet WiFi 1.02 or later + DueX5
Board ID: 08DGM-956GU-DJMSN-6J1DL-3SN6M-TTNRF
Used output buffers: 3 of 24 (12 max)
=== RTOS ===
Static ram: 27980
Dynamic ram: 94488 of which 60 recycled
Exception stack ram used: 264
Never used ram: 8280
Tasks: NETWORK(ready,384) HEAT(blocked,1224) DUEX(suspended,160) MAIN(running,1824) IDLE(ready,80)
Owned mutexes: WiFi(NETWORK)
=== Platform ===
Last reset 00:00:13 ago, cause: software
Last software reset at 2020-05-20 10:19, reason: Stuck in spin loop, spinning module Move, available RAM 7880 bytes (slot 2)
Software reset code 0x4084 HFSR 0x00000000 CFSR 0x00000000 ICSR 0x0041f80f BFAR 0xe000ed38 SP 0x200042e4 Task IDLE
Stack: 00454cdd 0045570c 61000000 a5a5a5a5 00454cdd a5a5a5a5 20004308 200041f8 00000002 2000512c 00004be2
Error status: 0
MCU temperature: min 31.3, current 32.4, max 33.3
Supply voltage: min 24.3, current 24.4, max 24.6, under voltage events: 0, over voltage events: 0, power good: yes
Driver 0: standstill, SG min/max not available
Driver 1: standstill, SG min/max not available
Driver 2: standstill, SG min/max not available
Driver 3: standstill, SG min/max not available
Driver 4: standstill, SG min/max not available
Driver 5: standstill, SG min/max not available
Driver 6: standstill, SG min/max not available
Driver 7: standstill, SG min/max not available
Driver 8: standstill, SG min/max not available
Driver 9: standstill, SG min/max not available
Date/time: 2020-05-20 10:19:45
Cache data hit count 21289392
Slowest loop: 3.01ms; fastest: 0.13ms
I2C nak errors 0, send timeouts 0, receive timeouts 0, finishTimeouts 0, resets 0
=== Storage ===
Free file entries: 10
SD card 0 detected, interface speed: 20.0MBytes/sec
SD card longest read time 1.5ms, write time 0.0ms, max retries 0
=== Move ===
Hiccups: 0(0), FreeDm: 169, MinFreeDm: 169, MaxWait: 0ms
Bed compensation in use: none, comp offset 0.000
=== MainDDARing ===
Scheduled moves: 0, completed moves: 0, StepErrors: 0, LaErrors: 0, Underruns: 0, 0 CDDA state: -1
=== AuxDDARing ===
Scheduled moves: 0, completed moves: 0, StepErrors: 0, LaErrors: 0, Underruns: 0, 0 CDDA state: -1
=== Heat ===
Bed heaters = 0 -1 -1 -1, chamberHeaters = -1 -1 -1 -1
=== GCodes ===
Segments left: 0
Movement lock held by null
HTTP is idle in state(s) 0
Telnet is idle in state(s) 0
File is idle in state(s) 0
USB is idle in state(s) 0
Aux is idle in state(s) 0
Trigger is idle in state(s) 0
Queue is idle in state(s) 0
Daemon is idle in state(s) 0
Autopause is idle in state(s) 0
Code queue is empty.
=== Network ===
Slowest loop: 15.62ms; fastest: 0.00ms
Responder states: HTTP(0) HTTP(0) HTTP(0) HTTP(0) FTP(0) Telnet(0), 0 sessions
HTTP sessions: 1 of 8

• WiFi -
  Network state is active
  WiFi module is connected to access point
  Failed messages: pending 0, notready 0, noresp 0
  WiFi firmware version 1.23
  WiFi MAC address 5c:cf:7f:76:68:e0
  WiFi Vcc 3.42, reset reason Unknown
  WiFi flash size 4194304, free heap 25200
  WiFi IP address 192.168.1.101
  WiFi signal strength -43dBm, reconnections 0, sleep mode modem
  Socket states: 0 0 0 0 0 0 0 0
  === DueX ===
  Read count 1, 4.47 reads/min

@dc42 I installed the internal build for 3.1.1 -18b8 last night and am still having the same disconnect problems.

I don't know how to reproduce the problem as it's intermittent and I haven't been able to find a cause yet. I haven't bothered to run any macros or prints yet as I'm trying to get the printer working correctly first.

Here's my current config.g file

config.g