Stopped Minoxidil and had head shaved for FUE transplant. Native hair not growing back.

If you stopped minoxidil and noticed hair loss, it probably means it was working.  If you stop using minoxidil then the hairs you gained will fall out over time.

It is possible to say that minoxidil was having positive effect on your hair and as a result of quitting, you are having some difficulties for hair growth.On the other hand it is possible to wait some more time to see if this lack of growth is temporary or permanent.

I'm not sure why your native shaved hairs are not growing back after stopping the minoxidil.  I would continue to watch and wait as they may just be slow to grow and will likely fill back in.  If not you can consider restarting minoxidil, or perhaps a better option for helping your other areas of hair loss, consider PRP or SVF cellular therapy.