Updating the flatpak causes theme settings to revert
When you update the flatpak from flathub you theme choice and settings are overwritten by the default.
It's not about the flatpak but about the update in any form, in this moment all the files are changed very quickly as I am still trying to find the best general config and troubleshooting on a modified configuration can be hard.
It's in the future plans however to avoid their overwrite.
This is currently worked around by #180. The downside to this is that if there are any major changes between versions that break things, the user will need to --reset manually rather than it happening at upgrade. (or if we know something will break, we can automate the reset beforehand based on version changes. It will still be the shotgun approach of resetting things).
This should no longer be an issue as configs are not force-overwritten on update anymore.