The original plan was for Chakotay to keep his baby that he fathered with Seska, and take that baby back to the Alpha Quadrant. Not sure if Seska was going to chase him to get her kid back, or she was going to rejoin the crew, or maybe no one is sure, because Jeri Taylor put a Nix on the idea of two babies on Voyager.
Basics was split between season two and three.
Jeri Taylor was not a producer in season two, but was a producer in season 3.
The producers/writers of Basics Part One thought that Chakotay was the father, and constructed the episode accordingly.
Once Jeri was in charge in Season 3, she suggested to her employee, the author of Basics Part 2 to have it that Chakotay failed a paternity test with Sesk's baby, because she thought that was best for Star Trek.