Today I updated the app from flatpak and all of my saved hosts are gone. Luckily I had these synced to my other computer, so I didn't lost anything. Also, the shadow is a bit strange.
So, I found a small workaround: Go to Preferences and enable encryption, then exit the app and replace the config files with your backup.
It seems like the app settings got reset on update and it didn't recognized the original config files.