Hi nemesis, welcome to the forums!
I’m sorry to hear this issue is affecting your save. As Shokujin mentioned this is one the team are aware of ( [Known Issue] Deconstruction of raft bases ) and has affected rafts for a while but may not affect every save. Is this your first save or have you had others where this was not an issue?
The team are investigating this issue but unfortunately we do not have a workaround for it at this time.