You can not directly change a via into a “MNPTH” (Whatever that is).
A lot of information in Gerber files is usually just missing, and there are no such things such as pads and footprints in Gerber files.
The way to repair this is to just delete the copper features representing the pads and via’s, and then place brand new footprints at the right locations. You can snap a pad of a footprint to the endpoint of a copper track.
Some time ago I made quite a long tutorial for this in:
“Mechanical” in “NTPH, Mechanical” seems to be explanatory: Non-plated through hole, i.e. mechanical hole (not electrically conducting). Usually the only reason to use a NTPH hole is mechanical: a screw hole, fastener hole etc.
In practice it’s possible to use a plated hole for mechanical purposes, but there’s no “mechanical plated through hole”.