I face the same problem - the solutions QB has lined out DO NOT WORK - unless I am missing something if you have posted an EXPENSE (not a bill), then I can't use their steps successfully. The only way I have found to get the credit back into the Project section for the way I am recording things is to make the deposit come back to the customer/project. So I put the customer/project name in the received from area, and then in the memo - I say it was for a refund from Home Depot or whatever it was. But in my use of QB Projects -  I do not bill the customer, it is only for record keeping of income/expense for the specific project. Not sure if it will work for you.