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. 

These do not always return, especially if they had been weak/miniaturized before the procedure. The shock/trauma of a transplant may have been the last straw for them. Still, a follow up with your doctor is not a bad idea. 

You need to see your doctor to find the cause of your hair loss.  Using minoxidil slows down the loss of native hairs. When  you stop using a product the hair that was not lost from using the product, will shed.  Some times this happens at a rapid rate and leaves a bold spot. 

I was one minoxidil and after, the native hair never grew back. It is very difficult to determine what has happened to you without having examined your prior to the process your summarized. Time may be one your side, so wait it out. Go back to your doctor who over viewed the entire process and ask him about your miniaturization studies and bulk measurements that he did to understand what will happen to you.These pre-op studies will be very helpful in predicting what will happen to you. 

I would recommend you to stay on the minoxidil. Get back on it.  The FUE is not in place of minoxidil.  Minoxidil thickens the hair shaft,  extends the growth phase of each hair and helps slow the loss of your surrounding hairs.  The transplanted hairs will not begin growing for at least 6 months.  They need to regain blood circulation by connecting to the vasculature of the recipient area. This takes time.