If Hazel’s App Sweep function stops working for you, a backup drive (or folder) might be the problem. Hazel automatically ignores Time Machine volumes but other backups, such as a Super Duper clone, can trick Hazel into thinking the App is still installed.
As of writing this, there’s currently no way to ignore volumes or folders in the Hazel interface but there is a hidden preference for it that you can access easily though the Terminal.
Running the following and restarting Hazel solves the issue:
defaults write com.noodlesoft.Hazel IgnoredBackupDirs -array dir1 dir2
If you want to ignore a backup drive or your path has spaces in it the command you run might look like this:
defaults write com.noodlesoft.Hazel IgnoredBackupDirs -array "/Volumes/SD Clone"