Hi Michael,
Safe Clean deletes directories that apps have left behind. It should not delete any folder created manually by user unless they have exactly the same name. Let us know what was the full path of your deleted folder.
We will check directories created by Mega app and update our app database to enable Safe Clean to work correctly with it.
Have you tried to turn on Safe Clean Check yet? Maybe it can provide you with the customization you need. Let us know please.