Editing/Hacking 8031 Eprom code
What you're proposing sounds absolutely feasible. You're not talking jibberish! If there's unused space in the main EPROM, you can patch the code to jump out of the main part into a small routine in the presently-unused part, and jump back again.

You will probably need to disassemble the existing 8031 code to determine where to apply the patch. You may be able to modify the existing code without changing its size. Or you may be able to overwrite instructions with NOP (no-operation) if the new code is smaller. The logic in the EPROM may do some sort of test to make sure that no more than 47 samples are used. You'll need to find all the places where this test is done and increase the 47 to some higher value.