Could the file system have been changed with the Catalina update, and not converted back when restoring the backup?
Case sensitive files systems are not supported; I think case-insensitive APFS is default since High Sierra (HFS+ case-insensitive before that), so that probably isn't the problem if you didn't change it. You can double check in Disk Utility (/Applications/Utilities).
I'm not sure what else could have been changed, and not affected by restoring the backup, unless there was something not backed up, or a setting not restored.
An automatic update of a security program, etc, in the backup could re-introduce a conflict that wasn't present when the backup was created. In that case, most likely the clean boot would have helped, though.
A hardware issue could cause this type of behaviour, but then I wouldn't expect the symptoms to be so specific.
