Ponding water on a roof is never good. Combined with bad flashing calls for a disaster. One of the methods to remove pooling from a flat roof is to cut a channel into the roof towards a scupper or a drain.
So many roofers have tried to patch this roof by smearing tar and doing all sorts of repairs but never addressed the issue. Water was pooling against the window flashing and perimeter and there was nowhere to remove the water effectively.
We decided to cut a channel towards an existing scupper. This worked out very good and the owner has been happy ever since.