duplicates

Where are you seeing the duplicates? In the Photos library itself in the Library/All Photos view?

If that's where you're seeing them then the following may help: 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 - $29.95  

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 - $9.99 - 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.

You do not want to go into the library's package and remove./edit files in there. It's not designed for user access and any changes can damage and corrupt the library. All changes should be made via the Photos app while viewing the library.

How are you trying to merge the libraries? Photos is checking for duplicates on import, but can only detect exactly identical files. When you merge libraries by exporting from one library and importing into another library, you need to export the unmodified originals, or Photos cannot recognise duplicates.

Do you still have the original iPhoto Libraries on your system volume? Photos is saving storage when it is creating a Photos Library from an iPhoto Library by creating hard links to the files that are appearing in both libraries. Together the new Photos Library and the old iPhoto Library are sharing the storage for identical files. But these hard links may no longer work, when you merge the libraries by exporting and reimporting. When the hard links are broken, you may all of a sudden need twice the storage. I would remove the iPhoto Libraries to an archive drive, if they are still on your system volume.