Manually remove all but one duplicate copy making sure that you only remove from Library, not from computer.

https://www.mediamonkey.com/support/knowledge-base/mediamonkey-database/why-are-there-duplicates-in-the-library-and-how-to-fix/

Hello,

some of my files are shown duplicated even though they refer to the same physical file. How can i solve this issue?

I am using 4.1.30.1914 on windows 10 64.