As long as it tells you what the unit was that it couldn't update and was deleting, I would be fine with that rather than a scenario I can't update. I am familiar with the messages it provides after the update happens where unit loads for aircraft are not correct, and simply correct that. In this case if it told me it couldn't update a certain ship, I could just get the ship from the updated DB and reconfigure it.
As I mentioned when I reported the error however, in order to figure out what potential unit was causing the error when I first got it, I systematically deleted one side after another in the scenario, hoping that once the culprit side was gone, I could reload the full scenario and focus on the various units on that side until I found the culprit. But I ended up with a scenario that had nothing left in it (all sides were deleted), created a blank new side since I couldn't run the update without one, added nothing (basically a blank scenario), and the update still gave me that "Ship#0 not found" error.