Can someone tell me how to fix this, if it is fixable? [attach]102677[/attach] [attach]102678[/attach] [attach]102679[/attach] [attach]102680[/attach] [attach]102681[/attach]

I have some areas on my flat roof that are low. When it rains it puddles there. This new roof was installed (2 ply hot mopped) in 2015. Recently I noticed the low spots have began to "blister" (not sure this is the correct term). When I took a blower to it it kicked up a lot of sand and black stuff then I see some bald spots. Called the roofing company out and they said the only way to repair this is to put more asphalt paper over the low areas, then another sheet over that but smaller, then another sheet, so basically build a pyramid to create a high spot. They will make a rectangular pyramid composed of a slightly smaller sheet for each layer. Is this the right strategy? The low spot shape is irregular. So if you lay a rectangular sheet down, you just raised the outside again, and so the inside spot will be lower by the same amount. I guess I don't see how this would solve the problem. I am thinking if there is some sort of self leveling liquid that can be poured over this to level the whole thing, then another ply can be put over the whole thing to seal it off better?