James, so long as they total up to $0, it really should be fine.
Let me look into it from our end. I tried an example of $100 positive, and $100 negative and it worked perfectly. Perhaps with the number of items and number of expenses, it is getting upset somewhere.
I'll let you know what I find out, but in the meantime, keep moving ahead, because it really should allow a $0 balance to go to QuickBooks.
Paul