This Makefile you are mentioning about does not seem to exist.
What I think happened is that the first upgrade executed dkms and this failed to build the nvidia kmods, but dkms thinks it was built and installed correctly.
Do this:
- dkms build -m nvidia -v 346.72 -k $(uname -r)
- dkms install -m nvidia -v 346.72 -k $(uname -r)
- xbps-reconfigure -f nvidia
Before running xbps-reconfigure, make sure the kmods are built and installed correctly.