Put down a thin 1/4 in layer of plywood over any soft spots on the roof. Go around the edge of the plywood with bondo all purpose. Paint over the whole roof with 1 Gallon of Heng's Rubber Roof Coating (on Amazon for $55/gal) and use ProTapes Pro Flex Flexible Butyl All Weather Patch and Shield Repair Tape, 50' Length x 2" Width ($22 on Amazon) on all the seams. You will have a waterproof roof.
BTW: if you do not mind the tedious process of installing it. Use some DOUBLE Bubble Aluminum Reflective Insulation Roll for insulation instead of the fiberglass that soaks up and holds moisture.
You can spend more money but one gallon of Hengs should do your whole roof. The Plywood is just to make the soft spots strong enough to walk on. I did not even bother to remove the old EPDM. The bondo will stick to the EPDM but is rigid and it will not flex, so cover the seams/edges with the tape if you ever want to move the unit. Hairline cracks will appear in the bondo at the seams.
Another BTW: If the roof membrane is white on top and bottom it is a TPO membrane not EPDM. EPDM is white on the one side and black on the other. Not all coating material will stick to TPO but Hengs will, which is why I recommend it over the $300 dollar stuff (liquid rubber) that also needs a primer coat before it will stick to TPO.