So after multiple drive switches my Time Machine suddenly stopped backing up system folders. I looked into /Library/Preferences/com.apple.TimeMachine.plist and indeed there is under ExcludedByPath /Applications, /System and so on. I have tried deleting it however the time machine always restores the exclusion path. I have tried copying it to desktop and removing exlude by path value but it still got restored to original value. Any ideas on how to fix this ?