If you add a ship to a trade fleet in a spot, you should be able to move the fleet out and back to update the trade route. A few posts also mentioned that the trade route will be correctly updated at the end-of-turn.
The serious problem happens when you remove a ship from a trade fleet in a spot. I didn't try disbanding them one at a time, but having been forewarned, I made this mistake only once with a three-ship stack (I needed the fluyt in the stack to reinforce my naval stack in a fight, forgot the bug).
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