Firstly, there is no way to select an invoice to work with until you've entered all the payment information. The "Invoice Number" field at the very top of the screen simply pulls in the customer associated with that invoice. This is a convenience feature since many checks include the Invoice Number but not a Customer ID.
 
To fix it, what I would try (I'm pretty sure it will work) is to enter a check number that is different. I believe it will say "Check number not found on that date, continue?" and will let you proceed. I would use the original check number with a -B or -2, etc.