It had been leaking into the apartment below us. Make sure you can lift deck sections so you can clean underneath. Put soft pads between the deck and the roof membrane. If it is modified bitumen we have had excellent results with a quality outdoor carpet instead of building a wood deck that will warp and rot eventually.
Carpet is inexpensive, fast, and easy to keep clean.
Many times looks better than a wood deck. If it is not subjected to high wind and you need to cut it around posts it will probably stay on the deck loose laid. If the corners blow up then use carpet tape that is compatible with the roof membrane, most are compatible. Does not raise the roof deck causing a conflict with doors or raising snow level up against doors. Send more details we may be able to help more.