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Your question is very complex, and may be more than can be answered in an on line forum
Is it possible that and unresolved pinched nerve in the ankle Achilles area could cause constant pain that becomes neuropathic and spread to other joints and even lead to migraines
That is very unlikely. while their are a few nerves in the area, they are very small by the time they have traveled that far, and do not have any ability to "spead" any thing upward except simple information about pain and temperature in foot, etc
Your daughter has had many complex and advanced interventions and medications. A pediatric neurologist will have some expertise in treating her headaches, and may have some help for the other pain.
If she has not had an MRI of her brain and spine, she should to be sure that there is no treatable problem. If she has not had a sleep study, that should also be done, as poor sleep can cause a multitude of problems.
Good Luck in your efforts. I hope this helps