I have done a few experiments in this direction and generally don’t bother with drill files.
The whole concept of “footprints” hardly exists in the gerber files, and therefore I do not even try to reconstruct it, because it’s very easy to simply use new footprints.
So I just throw away all the re-imported pads, then recreating the schematic and position new footprints over the ends of the existing tracks.
I did a write up about that (which still needs cleanup) and posted it: