Hi,
I have made a fix that will hopefully fix both of these errors (the file system access, and changing the preferences) here: Permissions by ptomato · Pull Request #5 · flathub/com.inform7.IDE · GitHub
These issues were both due to Flatpak sandboxing.
Once the test build finishes, I’ll merge it right away. After that happens, if you update with flatpak update or your software center then it should work properly.
I hate to keep asking for everyone’s patience, but I’m still working off and on at porting the IDE to use more modern versions of the dependencies so that we don’t have to use such an old version of the Flatpak runtime.