Note that rebuilding the file won't solve the issue and is completely unrelated to the problem. It's a known issue and there is no solution.

When I finally got to a useful person in tech support, they didn't attempt to have me rebuild the file because, and I quote, "What would you that do? This has nothing to do with a corrupt company file."

Using the new Undeposited Funds account is the only way to move forward once the program makes this decision for you. The sooner you make it your default account and get your old account back to $0, the sooner you can just do business as usual, albeit with a randomly created new account.