I understand how challenging this is for you, @ATARS. Please know that this isn’t the experience we aim to provide, and I appreciate you bringing it up. Let me share some insights to help with the situation.
Before anything else, can you clarify which page in QuickBooks you’re using to try and link the project to the deposit?
Projects should link as long as they’re marked as “in progress,” whether you’re connecting the deposit from the Bank Transactions page or through the Bank Deposit screen in QuickBooks.
Also, when entering the deposit, ensure you're selecting the specific project in the Customer/Project, not just the customer’s name. If you select only the customer, the deposit might link directly to them instead of the project.

Let me know if you have any other questions or need further clarification.