Summary
The Plover config file is emptied when the disk is full.
Reproducing
It's necessary for the disk to be full to reproduce the issue. I think the only easier way to do this is to make a tmpfs and edit the source code to write the config file there.
Plover Version
Plover 4.0.0.dev8.
System
Arch Linux.
Currently, Plover truncates the file before writing to it. It's possible to write to a temporary file and move it to the original location instead.