Gallery shows all pictures that can be found on the phone - it has no "place" to keep pictures, so you can't "delete it from Gallery", you either delete it from storage or you don't.
If there's a folder in which you keep certain pictures, and ALSO a folder in which you keep all pictures you took while on vacation, in addition to having 2 copies of the same picture, deleting one will still leave the other one for Gallery to find.
But bear in mind - there's no "place" called Gallery" in the phone. Gallery is an app, that's all. If there's a picture somewhere in the phone (except for those marked "do not show"), Gallery is going to show it. So you can't delete a photo "from Gallery". Use a file manager, find all the pictures that are the same (you'll notice that the last name in the chain of folders is the "album" Gallery "shows" the photo in) and delete all but the one copy you want to keep. Then back that copy up to a) your computer and b) a cloud account. Just to be sure.