I’ve recently had a similar issue, anything inside the categories would not work, scripts, chunks, plugins.
After moving them out and returning a month later I found this option in system settings:
Check Category Access - Use this to enable or disable Category ACL checks (per Context). NOTE: If this options is set to no then ALL Category Access Permissions will be ignored!
I changed that to no and everything worked well again.
I’m not sure what the issue was as I am the only user and not access restrictions were changed.