The question really depends on whether your job is as a professional pilot or as a member of the Army. The IRS argument is likely to be that even if you lose your medical, you will still be paid by the Army in your current grade, and reassigned to do something else.
This has been fought many times, with different results. It would help if you could show some outside employment as a pilot.
That said, I would take the deduction, and risk the audit. The IRS appears to be underfunded this year, and you are not risking jail, just a small financial penalty. Talk to a tax professional, (not H&R Block).
Joe