Flat roof ponding near drain - should roof be raised?
2" deep puddles on a flat roof are a definite problem, and imply at least 16 feet of problem if the minimum 1/8" slope to drain is to be restored/preserved/maintained. And if that makes new puddles, even more area needs to be fixed.

I'm not clear on your (non-described) process, but this mess seems ripe for building up a proper surface with rigid foam and a new membrane, rather than jacking the roof boards from underneath, if that's what you have been doing.

Regardless of process, the entire roof surface needs to slope at least 1/8" per foot towards the drains. No part of the roof should actually be "flat".