I'm thinking that Photos sees two different Libraries: the one on your Mac and the one on the hard drive. You don't say if you're connected to iCloud Photos, so I'm guessing that's not part of the deal. You also didn't mention which macOS you're using, so what to do may depend on that.
To see all your Libraries when the hard drive is connected, you should close Photos, and option-click on the Photos icon. Then you will get a dialog that shows all the Libraries that Photos knows about. This is what it looks like for me:

I can see that my Favorites Library is the one that is the System Library, but the Nikon Library is the last one I opened.
If you are seeing two different libraries, you can import the pictures in the new Library using the Import dialog. If you want to preserve the albums and folders on the other Library, you may want to try the 3rd Party app PowerPhotos ($30) -- it makes handling multiple Libraries a lot easier, and it offers a number of helpful operations for Photos-- Lots of us use it a lot.
Let us know if this is what's going on!