The Flatpak package uses a different path for storing bottles.
Migrate to Flatpak
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.
Migrate old bottles to Flatpak
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 \
# or move (using rsync to take care of existing files)