Migrate directories to Flatpak
The Flatpak package uses a different path for storing bottles.

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 data directory: ~/.var/app/com.usebottles.bottles/data/bottles.

The migration is simple as it sounds - just move (or copy) the content of the path ~/.local/share/bottles to the new one ~/.var/app/com.usebottles.bottles/data/bottles
# make a copy
yes | 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.
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Migrate to Flatpak