Hi.
I've been facing this issue for a couple of weeks now. My system is Manjaro Linux with Xfce 4.18 and I'm using Geany daily. (BTW I also have saved my Xfce user session to find back my windows where I want them to be).
I've noticed when I boot my system, sometimes, on random occasions, Geany's configuration has been overwritten with the defaults. It doesn't occur everytime I shut down my system, only randomly and _I haven't been able to find a pattern_. This is really annoying and the only way I've found so far is to restore my configuration from a backup.
I'm using a single F2FS filesystem on a NVMe drive, except for `/boot/efi`, which as required is located on a VFAT filesystem. I have no idea if this is important though. Geany is version 2.0, built 2023-10-23.
Cheers, π