If there is no moisture in the roofing system and none of the previously stated conditions exist that would dictate a complete removal of the system then just check the waterproofing layer. Can the waterproofing layer be left in place? If it is a single-ply membrane then most manufacturers allow the membrane to be left in place providing it has no contaminates (oil/grease) and is sliced into a 10′ x 10′ grid. The two explanations we have heard for slicing the membrane are that it either relieves the tension in the system or it prevents a vapor barrier from being in the middle of the roofing system. (Side note: we have seen a few instances where a polyethylene vapor barrier was actually placed on top of an existing roof and new insulation/membrane installed above. This invariably kept the bottom roofing system drier and even prevented water leaking on the tenants, but spread the moisture throughout the top roofing system – likely causing it to fail sooner.)
If the single-ply waterproofing layer cannot be left in place or sliced and left in place then it should be removed. If the system is asphalt based without gravel (modified bitumen or bald asphalt) then usually no extra measures need be taken – another roof can be placed on top. If the system is asphalt based with gravel (asphalt/tar/pitch and gravel) then the gravel should probably be removed. We have seen many roofing systems where the gravel was left in place, insulation mechanically fastened and EPDM installed, with no adverse effects. We have seen a few instances where the same scenario produced tenting fasteners – but it is hard to say if the fasteners tented due to a poor roof deck, water in the bottom roofing system or the gravel shifting a little as time went on. If a second roofing system is being put in adhesive over an existing roof with gravel then the gravel and dirt must be wet vacuumed off to obtain a good bond.