Photo FOLDER duplicates

If they refer to the same files, that's why they would both delete. Otherwise there may be corruption in your library file.

Mac OS X Photos manages albums using what are called XML files. XML is very similar to HTML, in that <tags> are described within greater and less than as shown, and their descriptive contents are between starting markups and ending markups.

What I recommend you do is check the contents of the albums and decide if they are in fact different from all other albums before trying to delete. Otherwise it may think you are trying to delete a the same album from two different places.

If you tell it you want to delete from the Library, it will delete the photo from all albums. If you simply edit menu -> cut a photo selected from an album, it will delete it from that Album.

Anything inside your Users -> yourname -> Pictures folder is managed by the Photos App, unless you tell the App not to manage your photos. Attempting to modify the content of a managed folder can conceivably create the side effects you are seeing, especially if you manage it via the Finder.

OK, that's a horse of a different color. Libraries and Albums often point to the same originals. One way to make sure you aren't deleting the only copy is to show in Finder both images to make sure they aren't pointing to the same original. If you want to duplicate a photo to keep an original with specific color and brightness metadata, always go the Image menu and select Duplicate. or hit command-D. Rename the duplicate an entirely different name so you know you can edit that one, while keeping the original. Smart folders and albums are in fact just pointers to the same original but with specific search criteria.