In recent versions of the Flatpak and, the bottles are saved in a different location than the other packages, respecting the structure of the Flatpak package.
The other packages save the essential Bottles files, such as components, temps, and bottles, in the directory:
~/.local/share/bottles . Flatpak saves these files in the Flatpak
The migration is simple as it sounds - just move (or copy) the content of the path
~/.local/share/bottles to the new one
# make a copyyes | cp -rf \~/.local/share/bottles/* \~/.var/app/com.usebottles.bottles/data/bottles# or move (using rsync to take care of existing files)rsync -a \~/.local/share/bottles/* \~/.var/app/com.usebottles.bottles/data/bottles
Restart Bottles and that's it.