3 years later, and I've recently encountered the same issue on my Duet3D 6HC mainboard. Config.g and config.bak are deleted, yet there is the a new config.g file dating back to when we first started the mainboard last year - has the generic 5-6 lines of code.
All other files for homing the axes and all gcode files of previous jobs are still on the card. We've even printed sth about 4h prior to the deletion of the config files.
We also had that 2_test_macro preinstalled at from when we bought the Duet3D.
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RE: Deleting config.g file