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Sorry for the trouble! If OmniDiskSweeper is asked to delete a file, it will ask "Are you sure?" and if the person using it says "Yes", the files will be deleted. It doesn't delete anything automatically or without asking for permission from the user, in other words.

In this case, it sounds like something that probably shouldn't have been was selected within the app and deleted. If you have Time Machine or some other backup system in place, that would be the way to recover from something like this.