When I redid the roof on the 5er I replaced the EPDM and sheeting.
I had a leak by the air conditioner. When I took the rubber off about half of the sheeting was bad or badly discolored by mold. I did not want any mold in the unit so I replaced all of the sheeting as well. I replaced the chip board with plywood and then put a new membrane on.
I did it pretty much by myself. Janet helped me lift the EPDM roll onto the roof.
I had a shed to work in and lots of time. I did not rush so it took me about a month with doing other tasks as well (grass mowing, gardening, etc).
One thing I found was the insulation could have been put on better. I filled all of the empty or thin spots and cleaned out all of the wood shavings and debris.
IMO this is not a job you want to cut corners on.
In your case you should be able to cut an area out of the membrane and check the sheeting. Replace as required. Go back as far as you need to and then get a piece of TPO or EPDM. There are lots of sealing tapes to join the old and new membrane. Lots of instructions on the web.
Gordon and Janet
Tour 42QD/inTech Stacker