Flotsam seemingly only spawns once after the player has discovered the Sunken Boat, and then despawns forever. This makes destroying the Sunken Bot the only option if players want the trinket to create the Seaworther.
Steps to Reproduce
Make a save file, make it RoG and SW compatible. Find the Sunken Boat and then come back to it a few days later. Flotsam ceases to spawn from that point on, though I may be wrong.
This issue has not been confirmed by a developer yet.