Based on the information you provided and according to my interruption of AR 350-1, if the test was specified as a For Record test it must count. As an exception to this statement, if the test was administered outside the guidance of the command’s policy they could determine the test does not count. For example, local policy could demand that only certain trained/certified individuals may administer the APFT for the sake of maintaining Army Standards. If you were given the test by someone who was not certified then yes, the command could void the test.
I would encourage you to sit down and calmly speak with your chain of command in a professional manner to determine why they believe the test should be voided. If they decide to void the test you must then ask yourself another series of questions. Is this worth fighting over or is it simpler to just to take another For Record APFT? If there is a difference of professional opinion it may be better to let it go. Did you take the test in accordance with Unit requirements?
AR 350-1, page 11, paragraph 1-24b(2):
Commanders may administer the APFT as often as they wish; however, they must specify beforehand when the results are for record. The AA and Active Guard/Reserve (AGR) Soldiers will take the APFT at least twice each calendar year. A minimum of 4 months will separate record tests if only two record tests are given. The intent is for the Active Army and the AGR Soldiers to take a record APFT every 6 months. Mission requirements often prevent the even spacing of record tests. Therefore, commanders are encouraged to test Soldiers for record as close to the record test window as possible.
Thanks for the kind words. We try to provide relevant answers for Soldiers and Leaders using our experience and regulatory guidance, but our main goal is to encourage Soldiers and Leaders to speak with their chain of command to solve issues. The solution to problems is usually found at the lowest level. If it cannot be solved there, take it up the chain of command and find someone who will help.