@BelgarionNL - you said you created the duplicates by moving them from another library. Are these the exact same books, or slight variations (e.g. different formats, different versions of the same epub etc).
If they are binary identical, then you can use the Binary Compare search, and tick the box which automatically removes duplicates. That will remove the book format files, but still leave you with the book rows in calibre. If indeed those rows were created purely from identical copies of the book then one of each of those duplicate pairs will now have no book formats associated with it. So you can do a search for formats:false and then delete those to finish the cleanup operation. The plugin does not automatically do this because there might be metadata on those rows (like a better cover) that you may want to keep by manually merging them.
However if the books you merged in are not binary identical, then it is entirely up to you to go through one by one and decide which version of a format you want to keep. There is no tool on the planet that can make that decision for you - only a human eyeballing them can decide which one is of better quality since it is so subjective.