There is all manner of unknown (to me) stuff in %appdata% and %program data% and this would be copied.
For example my Mail App data (local emails) is here (thanks Kari Mail App - Backup Email Messages in Windows 8 )
and I expect Music App stores something here but I don't use that app.
It is only really an issue if you have moved the files to which it refers. It should be updated but obviously not always. I wouldn't worry about it and certainly re-installing is safer than trying to figure out what to delete.