And just to be sure, can I delete the Sales Receipt without refunding the actual payment? Basically, keep the money but delete/void the record of the "extra" sale?

I was able to balance everything as-is by making a Credit Memo and matching the Sales Receipt to the bank Deposit instead of the Invoice. 

But my main question is: what is the best practice for requesting project deposits in QBO? Payment Link is nice because it doesn't require the customer to edit the amount like in the Invoice Payment screen. But maybe there's a better way.