I don't know why that would happen. Assuming mysterious corruption, a/k/a "gremlins".
There is no one single file, all those files actually do things.
You can, however, test with bringing back pieces at a time.
Custom columns are stored in the per-library database. Inapplicable.
plugins and plugin configurations (should be safe):
Code:
~/.config/calibre/plugins/${plugin-name}.zip # this is the downloaded plugin
~/.config/calibre/plugins/${plugin-name}.json # this is the configuration for the plugin
Conversion customizations are in:
Code:
~/,config/calibre/conversion/
Each file is a python dictionary of the settings. Should be safe.
Main menu: stored in gui.json under the key "action-layout-toolbar*" -- this file stores a lot of stuff, including things like window geometries. Possibly not very safe at all.