Using the create files in mod instead of overwrite should now function as intended.
Plugins and INI files will attempt to go to the correct location regardless weather or not the folders exist or not. Fallout New Vegas specifically was fixed as well with this. On top of this running fluorine in the terminal should now also report the location of where they are going:
[2026-02-18 06:16:09.115 I] Wine prefix paths: AppData/Local plugins dir='/home/USERNAME/.var/app/com.fluorine.manager/Prefix/pfx/drive_c/users/steamuser/AppData/Local/FalloutNV', Documents/My Games INI dir='/home/USERNAME/.var/app/com.fluorine.manager/Prefix/pfx/drive_c/users/steamuser/Documents/My Games/FalloutNV'
[2026-02-18 06:16:09.141 I] Using Wine prefix: /home/USERNAME/.var/app/com.fluorine.manager/Prefix/pfx
[2026-02-18 06:16:09.153 I] UMU launch: '/home/USERNAME/.var/app/com.fluorine.manager/umu-run' '/home/USERNAME/.local/share/Steam/steamapps/common/Fallout New Vegas/FalloutNV.exe' (game id: umu-22380, steam: '/home/USERNAME/.steam/steam')
[2026-02-18 06:16:09.160 I] Process helper: started 111188
Timestamp fix, wine calling SetFileTime() should fix the timestamps and allowing them to update.
FOMOD Images will now be displayed if they have them in the bundle.
fomod-plus-settings.ini will now go to the config folder of the flatpak instead of the home folder. ~/.var/app/com.fluorine.manager/config/