Giovanni,
I have no way of knowing what may have been put on your fiberglass roof, but it it is lifting I am sure it can be scraped off and/or sanded down. The only places the fiberglass roofs usually develop leaks is at the front and back cap seams, or any of the penetrations through the roof like AC units, skylights, refrigerator covers, antennas, or plumbing vents.
If the old coating needs to be removed a new coating of your choice can be applied over it. You might want to go see what the repair person is talking about for yourself, or get another opinion.
If it is not leaking and has no signs of leaks I would not be overly worried.