My mare used to be the same way. Every day I worked on slowly rubbing as close as i could to her ear until she gradually lowered her head. Years later there are no more problems!
Just go easy and be calm about it. Soft tones and be smooth. Also treats help!
I had a horse like that for awhile. I started my rubbing his back before slowly making my way to his face. It took time but now he isn’t head shy at all
I definitely recommend adding free riding into your riding routine. This will make the horse feel less pressured and more comfortable. Try riding with a halter and clip on reins, bareback. Good luck
Work slowly at it and be patient, don't push to hard. Start on the side of the horse as far forward as they will allow and just rub them until they relax then move a little bit closer and continue doing that.
You can start rubbing her neck and slowly move upward towards her head. Praise her when she lets you touch her head and work slow.