It turns out I have two instances of Flathub, one system installation and one user installation. The user installation has zero apps installed and I guess that one might have been created during my attempts to build programs with Gnome Builder. This leads me to believe that I should be able to delete everything under ~/.local/share/flatpak without any problems, after deleting the repo from the Purism App Store. Question is if it is enough to just delete it from the repo section, or do I need some other CLI uninstall?
EDIT: I have now removed the flathub user repo in the app store and deleted the entire ~/.local/share/flatpak/appstream folder with seamingly no problems, recovering another 4GB of disk space. I am now looking at the /var/lib/flatpak/appstream/flathub/aarch64 folder wich contains some 660 folders named “.1371b7418a5654528860eaec3df6e3f3261be5de861eeb63e75a3b76fc1fe03c-4TXNM1” etc, all containing three objects; appstream.xml, appstream.xml.gz and the folder icons. Looking into the icons folders, I find between 2500-3000 png files in two folders 64x64 and 128x128, weighing in at 35-45MB. That multiplied by 660 folders add up to 3.6GB in almost 860,000 objects!!!
Maybe a total flatpak wipe and purging everything flathub on the device, followed by a fresh flatpak reinstall of the 4 apps I currently use would clean out most of this space?
EDIT 2: I have now completely uninstalled flatpak and removed the associated folders under /var/lib and ~/.local/share. My free space is now 20 GB. I will likely reinstall flatpak at a later stage if needed and hopefully it won’t totally bloat my system again.