Export Gerber to PCB: vias and THT pads

I have exported a Gerber set to PCB, and I’m fiddling about how to get vias and pad holes. I think that it depends on the correct layer to assign as “holes” file. The only holes file in the set is a drill spec, which is not suitable. I “managed” to get vias on each edge of a line segmented text in both copper layers that are written at exactly the same location, but circles on both copper sides on the same location are kept as such.
In the docs, the term “flash” is used. Well, a circle is a flashed item in Gerber.

Upon comparison of a typical Gerber output by pcbnew and the external Gerber set, I see no Gerber version in the header. The %…% lines mainly consists of ADDxxR lines, for sure embedded aperture definitions.

The Gerbers are dated 01/2015. Hence I think that a conversion in a newer format could solve the issue. Any suggestions regarding tools or scripts are welcome.