doubled up on part extraction

See: https://musescore.org/en/handbook/3/parts#delete

in the parts-window, on the left, you have "delete", you choose what part (in MS 2.3)

For future reference though - don't think of the parts as having been "extracted" - we instead use the term "generated". it's just a word, but it might be the source of confusion here. Under normal circumstances, you should only need to generate parts once for any given score. Once they are generated, you can edit the score all you want and the parts are automatically updated, no need to generate them again. Somehow, I think the word "generates" connotes that a bit better than the word "extracted", which could somehow fool one into thinkin you need to do it over and over each time you make changes.

Anyhow, that's why when you do it a second time - an extremely rare thing to do - it doesn't replace the first set.