OK, I have to stop looking at this for the night, but where I've gotten so far is that some of the pads do not seem to get valid nets from eeschema during the "remap nets" portion of Eagle import (building the info to pass to fixEagleNets). So, before the two calls to FetchNetlistFromSchematic, the relevant pads have net "N$62", and after the calls, they have no net (!)
So, that net never gets included in the map to fixEagleNets and doesn't get propagated to the zones/tracks/vias.
But, if you then run the update from schematic command manually, the associated pads *do* get updated with proper net names. Of course, at that point it's too late for us to be able to know that we should go and update the N$62 vias.
I'm not sure why the pads are not getting nets during those update calls, but that's the smoking gun to look in to.
OK, I have to stop looking at this for the night, but where I've gotten so far is that some of the pads do not seem to get valid nets from eeschema during the "remap nets" portion of Eagle import (building the info to pass to fixEagleNets). So, before the two calls to FetchNetlistFro mSchematic, the relevant pads have net "N$62", and after the calls, they have no net (!)
So, that net never gets included in the map to fixEagleNets and doesn't get propagated to the zones/tracks/vias.
But, if you then run the update from schematic command manually, the associated pads *do* get updated with proper net names. Of course, at that point it's too late for us to be able to know that we should go and update the N$62 vias.
I'm not sure why the pads are not getting nets during those update calls, but that's the smoking gun to look in to.