If you remove a duplicate in the library it will be removed from every album, project, smart album in the library. Albums contain only pointers to the original file like music tracks in PlayLists.
If you don't want to wait for Photos to get thru comparing all of the photos in the library looking for duplicates you can take a pro-active role and try the following apps:
You want an app that will identify the potential duplicates, put them in an album or mark them with a keyword for easy retrieval and deletion by you. You don't want one that does the deletion itself for obvious reasons.
I've run tests on the these two apps with the following results and found them to be safe to use:
PowerPhotos - $40
PowerPhotos is the iPhoto Library Manager version for Photos and is very powerful. Although more expensive I would recommend it as it has more capabilities than the others like the capability to merge Photos libraries or copy photos, both original and edited versions, along with their metadata between libraries.
PhotoSweeper - $15 - Demo version available.
PhotoSweeper compares bitmaps and/or histograms so it can detect duplicate images even if they have different file sizes, file names, image sizes and capture dates.
Personally I prefer PowerPhotos as it's the premier utility for Photos libraries.
