When using the binary compare, you can check the option "When doing binary compare, automatically delete duplicate formats".
Note that this will only delete the book files (epub, ... etc) but will keep the entries in calibre (because it might contain metadata that some people would want to keep).
So, for entries that have only one book format, when calibre deletes the duplicate from them, they will be empty (i.e have no formats, just metadata). You can filter these using this calibre search:
Then, you can delete them, but only if you are sure you don't need the metadata form these empty entries. It is always a good idea to backup your library first just in case, especially when trying something for the first time.
For entries that have more than one format, I'm afraid you will have to delete the entries one by one.