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.