I found I didn't save my EEPROM. I fixed that by running a M502 and then M500. Saved my EEPROM, started a new print job.
I then did an emergency stop and the problem repeated itself: Once the firmware was restarted the printer was not seen by Repetier at all. No reconnection was found, could not activate, Repetier had to be reset in order to start printing again.
Here's some of the log of the job:
max_e_jerk>
> 3:03:45.722: echo: M205 B25000 S0.00 T0.00 X10.00 Y10.00 Z0.40 E5.00
> 3:03:45.723: echo:Home offset:
> 3:03:45.723: echo: M206 X0.00 Y0.00 Z0.00
> 3:03:45.723: echo:Material heatup parameters:
> 3:03:45.723: echo: M145 S0 H200 B60 F0
> 3:03:45.723: echo: M145 S1 H240 B100 F0
> 3:03:45.723: echo:PID settings:
> 3:03:45.723: echo: M301 P22.20 I1.08 D114.00
> 3:03:45.723: echo: M304 P690.34 I111.47 D1068.83
> 3:03:45.723: echo:Filament load/unload lengths:
> 3:03:45.723: echo: M603 L0.00 U100.00
> 3:03:49.647: Warning: Communication timeout - resetting communication buffer.
> 3:03:49.647: Connection status: Buffered:11, Manual Commands: 10, Job Commands: 0
> 3:03:49.647: Buffer used:11 Enforced free byte:0 lines stored:1
< 3:03:49.647: N1 M110
> 3:03:50.308: Firmware was halted, trying to reconnect. Eventually running print is stopped.
> 3:03:51.320: Error:Printer halted. kill() called!
> 3:03:51.395: start
< 3:03:51.395: M117 Finished
> 3:03:51.422: echo: External Reset
> 3:03:51.423: Marlin TH3D U1.R2.2
> 3:03:51.423: echo: Last Updated: | Author: (TH3D)
> 3:03:51.423: echo:Compiled: Sep 25 2018
> 3:03:51.423: echo: Free Memory: 3367 PlannerBufferBytes: 1232
> 3:03:51.467: echo:V55 stored settings retrieved (655 bytes; crc 32826)
> 3:03:51.467: echo: G21 ; (mm)
> 3:03:51.468: echo: M149 C ; Units in Celsius
> 3:03:51.468: echo:Steps per unit:
> 3:03:51.468: echo: M92 X80.00 Y80.00 Z400.00 E93.00
> 3:03:51.468: echo:Maximum feedrates (units/s):
> 3:03:51.468: echo: M203 X500.00 Y500.00 Z15.00 E50.00
> 3:03:51.468: echo:Maximum Acceleration (units/s2):
> 3:03:51.469: echo: M201 X1000 Y1000 Z100 E5000
> 3:03:51.469: echo:Acceleration (units/s2): P<print_accel> R<retract_accel> T<travel_accel>
> 3:03:51.469: echo: M204 P500.00 R1000.00 T500.00
> 3:03:51.514: echo:Advanced: B<min_segment_time_us> S<min_feedrate> T<min_travel_feedrate> X<max_x_jerk> Y<max_y_jerk> Z<max_z_jerk> E<max_e_jerk>
> 3:03:51.515: echo: M205 B25000 S0.00 T0.00 X10.00 Y10.00 Z0.40 E5.00
> 3:03:51.515: echo:Home offset:
> 3:03:51.515: echo: M206 X0.00 Y0.00 Z0.00
> 3:03:51.515: echo:Material heatup parameters:
> 3:03:51.515: echo: M145 S0 H200 B60 F0
> 3:03:51.515: echo: M145 S1 H240 B100 F0
> 3:03:51.516: echo:PID settings:
> 3:03:51.516: echo: M301 P22.20 I1.08 D114.00
> 3:03:51.516: echo: M304 P690.34 I111.47 D1068.83
> 3:03:51.516: echo:Filament load/unload lengths:
> 3:03:51.516: echo: M603 L0.00 U100.00
> 3:04:35.502: start
> 3:04:35.502: echo: External Reset
< 3:04:35.502: N1 M105
> 3:04:35.528: Marlin TH3D U1.R2.2
> 3:04:35.528: echo: Last Updated: | Author: (TH3D)
> 3:04:35.528: echo:Compiled: Sep 25 2018
> 3:04:35.528: echo: Free Memory: 3367 PlannerBufferBytes: 1232
> 3:04:35.572: echo:V55 stored settings retrieved (655 bytes; crc 32826)
> 3:04:35.572: echo: G21 ; (mm)
> 3:04:35.573: echo: M149 C ; Units in Celsius
> 3:04:35.573: echo:Steps per unit:
> 3:04:35.573: echo: M92 X80.00 Y80.00 Z400.00 E93.00
> 3:04:35.573: echo:Maximum feedrates (units/s):
> 3:04:35.573: echo: M203 X500.00 Y500.00 Z15.00 E50.00
> 3:04:35.573: echo:Maximum Acceleration (units/s2):
> 3:04:35.573: echo: M201 X1000 Y1000 Z100 E5000
> 3:04:35.573: echo:Acceleration (units/s2): P<print_accel> R<retract_accel> T<travel_accel>
> 3:04:35.573: echo: M204 P500.00 R1000.00 T500.00
> 3:04:35.621: echo:Advanced: B<min_segment_time_us> S<min_feedrate> T<min_travel_feedrate> X<max_x_jerk> Y<max_y_jerk> Z<max_z_jerk> E<max_e_jerk>
> 3:04:35.621: echo: M205 B25000 S0.00 T0.00 X10.00 Y10.00 Z0.40 E5.00
> 3:04:35.621: echo:Home offset:
> 3:04:35.621: echo: M206 X0.00 Y0.00 Z0.00
> 3:04:35.621: echo:Material heatup parameters:
> 3:04:35.621: echo: M145 S0 H200 B60 F0
> 3:04:35.621: echo: M145 S1 H240 B100 F0
> 3:04:35.621: echo:PID settings:
> 3:04:35.622: echo: M301 P22.20 I1.08 D114.00
> 3:04:35.622: echo: M304 P690.34 I111.47 D1068.83
> 3:04:35.622: echo:Filament load/unload lengths:
> 3:04:35.622: echo: M603 L0.00 U100.00
> 3:05:18.628: start
> 3:05:18.629: echo: External Reset
> 3:05:18.629: Marlin TH3D U1.R2.2
> 3:05:18.629: echo: Last Updated: | Author: (TH3D)
> 3:05:18.629: echo:Compiled: Sep 25 2018
> 3:05:18.629: echo: Free Memory: 3367 PlannerBufferBytes: 1232
< 3:05:18.629: N1 M105
> 3:05:18.675: echo:V55 stored settings retrieved (655 bytes; crc 32826)
> 3:05:18.675: echo: G21 ; (mm)
> 3:05:18.675: echo: M149 C ; Units in Celsius
> 3:05:18.675: echo:Steps per unit:
> 3:05:18.676: echo: M92 X80.00 Y80.00 Z400.00 E93.00
> 3:05:18.676: echo:Maximum feedrates (units/s):
> 3:05:18.676: echo: M203 X500.00 Y500.00 Z15.00 E50.00
> 3:05:18.676: echo:Maximum Acceleration (units/s2):
> 3:05:18.676: echo: M201 X1000 Y1000 Z100 E5000
> 3:05:18.677: echo:Acceleration (units/s2): P<print_accel> R<retract_accel> T<travel_accel>
> 3:05:18.677: echo: M204 P500.00 R1000.00 T500.00
> 3:05:18.723: echo:Advanced: B<min_segment_time_us> S<min_feedrate> T<min_travel_feedrate> X<max_x_jerk> Y<max_y_jerk> Z<max_z_jerk> E<max_e_jerk>
> 3:05:18.724: echo: M205 B25000 S0.00 T0.00 X10.00 Y10.00 Z0.40 E5.00
> 3:05:18.724: echo:Home offset:
> 3:05:18.725: echo: M206 X0.00 Y0.00 Z0.00
> 3:05:18.725: echo:Material heatup parameters:
> 3:05:18.725: echo: M145 S0 H200 B60 F0
> 3:05:18.725: echo: M145 S1 H240 B100 F0
> 3:05:18.726: echo:PID settings:
> 3:05:18.726: echo: M301 P22.20 I1.08 D114.00
> 3:05:18.726: echo: M304 P690.34 I111.47 D1068.83
> 3:05:18.726: echo:Filament load/unload lengths:
> 3:05:18.726: echo: M603 L0.00 U100.00