New comment by ericonr on void-packages repository

https://github.com/void-linux/void-packages/issues/27771#issuecomment-757062274

Comment:
flatpak stores stuff into `/var/...` and `~/.local/share/flatpak`, at least; maybe `~/.cache` as well. You can search for everything with `find / -name flatpak` (this can take a while).

That said, you usually don't want to run flatpak as root; just use the `--user` command line option whenever it complains about permissions.