This sounds like an issue that I've had to deal with. In our situation we have invoices with a related line items table. It would make sense to use the Invoice Number to relate the main invoice record with the Line Items record, but....
The invoices are printed on an NCR form that comes with the invoice number pre-printed. To make things worse, there are three printers with three sets of invoice numbers and no way to predict which tag will be printed on which printer.
So I had to define a serial number field that is hidden from the users and used it to relate my two tables. The invoice number became a value that was stored in a different field and was not added until the invoice was printed.
I suggest you do something similar. Use an auto-generated serial number to relate your tables and make your Protocol Number field a separate item. Now you can start populating your Table A fields before you assign a protocol number.