Screws packing out on roof deck, under the rubber roof

I would NOT cut the EPDM. I would install 2 x2 inch squares of eternabond over the affected screws. That will stop the screws from poking thru the EPDM and you have not affected the integrity of the EPDM. If you check the screws with your previous repair, I would verify they are WOOD screws and NOT self tapping screws. Wood screws rarely back up unless they have been stripped when installed. Doug