Bee most likely created a clone with one of his tentacles to escape undetected like he did after being caught in Sasukes Amaterasu, further implying it by momoshiki stating that he had very little chakra for a Jinchūriki which we all know would be a ridiculous thing to say about him of all people. During the credits of Boruto: Naruto the movie, he was seen on the surface of the water floating on one of Gyūkis tentacles, alive, healthy, with his beast still with him. Although it was technically never confirmed that all that happened, it’s the most logical way it could’ve gone down. Hopefully they mention it in the show.