Is there an equivalent low spot on the inside roof?
If not, the Sytrofoam inside the roof may be compressed where the dip is. If this is the case, it may be possible to drill a series of holes in the roof along the length of the dip, pull the dip out using some kind of puller, then fill the void with spray foam. After this, I'd seal the holes in some way. Perhaps fill with some sort of sealant (I like ProflexRV), then insert a screw into each hole; EternaBond perhaps?)
I would do all this after removing the vents and AC units. When replacing the vents and AC, I'd redo all the sealant between the roof and riser, and the riser and vent. Be sure to sandwich the sealant between each. (I've had terrible luck just sealing on top of things.
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