Deleting accounting records is always a poor idea. But this situation points out improper accounting procedures by your supplier. A true sales invoice should only be generated once, not added to subsequent invoices.
They may be doing what is called statement billing or statement accounting, where individual sales invoices are created, but their customer is sent a statement showing all invoices with balances remaining due, received payments, etc., with the net result being the amount owed after all invoices and payments to date. If that is what they are doing, just enter the purchase invoice for the new billing items. That way, you are not entering something a second time and deleting its original entry.
A convenient way to handle payments in that situation is to allocate the payment to
Supplier credits rather than
Accounts payable. Manager will automatically allocate the payment to the oldest invoices first.