How can I fight being separated for failing BLC after refusing to go because of migraines, and then being forced to attend anyways?

If you can't go to something that is required because of medical reasons, the commander can either bar you from reenlisting or request a med board. You have to be able to do what is required.

Going to turn it around a bit - You said constant migraines, so obviously you have gone to your primary care a number of times, were referred to specialists to determine the cause (don't know if they found an underlying cause for you) and if there was nothing to do, you were referred to a MEB.

At least, that's how it is supposed to work. Did you ever see your docs about it before BLC? Did you go to sick call while you were at BLC? If none of this is documented aside from a trip or two to the docs, then you did yourself a large disservice.

Having said that, are there routes you can take now? Yes. First, did you explain all this to your commander? At your counseling for the BAR, you should have been informed of your right to dispute or appeal the bar. I assume you have less than 10 years of service, so the rebuttal/appeal would go up to the first O6 to review. However, all of this without any medical evidence just sounds like you making a convenient excuse.

What you can do now? Two things - contact legal assistance and explain your situation. They can better advise you regarding steps about rebutting/appealing the bar (an appeal is done at the time of the BAR counseling normally). Second is that you need to go see your primary care and get the ball rolling about why you're having headaches. However, if there is nothing to show an underlying condition that is causing your headaches, it will just come across as that convenient excuse again.

Now, if you HAVE been going to the doc and have documented treatment, etc. you are in a much better position regarding the BAR. If you have been seeing the docs and they still can't figure out what's causing your migraines, then you should have been put on a profile limiting your activities and if they exhausted the 'limit of military medical care' and you still had constant migraines, you should have ended up in the IDES system for medical retention evaluation (and possible medical separation).

Bottom line: If you haven't already, talk to your commander regarding your migraines, and if you have, call legal assistance to see what your options at this point are.

That sounds like the consequences of your actions...

AR 635-200 para 13-2 Criteria for separation:
b. Commanders will initiate separation for unsatisfactory performance for Soldiers who are eliminated for cause from a Noncommissioned Officer Education System (NCOES) course. Commanders have the discretion to bar Soldiers from reenlistment in lieu of initiation of separation for these Soldiers per AR 601–280 or AR 140–111.