Q: Where is the application data folder? How do I backup my settings? How do I restore my settings?

FileBot keeps your setting in the registry, and keeps a backup of your settings in an
*.xml file in the
%APPDATA% folder which is restored from automatically on application launch if the registry is for some reason void of settings.

That means that something is deleting keys from the registry
and files from the
%APPDATA% folder. That would be most unusual and very concerning. You can investigate the issue by observing the registry and the
%APPDATA% folder yourself. If you notice unexpected changes, then some software running on your PC is making these unexpected changes. The likely culprit are misbehaving cleaner software, anti-virus software, etc.