Ref: AR 40-501, 7-9, d. (7)
quote:
(7) Upon the diagnosis of pregnancy, the Soldier is exempt from regular unit physical fitness training and APFT testing/weight standards for the duration of the pregnancy and 180 days past pregnancy termination.
So, if your wife took the APFT when she had not yet been
diagnosed by competent medical authority as being pregnant, and failed the run portion of the APFT, then was subsequently flagged, then she will remain flagged as a PFC for the duration of her pregnancy and 180 days after termination of the pregnancy.
The command may opt to have leniency if the projected due date is less than 9 months after the date of the APFT, since that would mean physiologically speaking she may have been pregnant at that time, but that is at their discretion.
Hate to say it, but it seems your wife may be stuck in the exact same situation my wife was stuck in a few years back. And yes, she had to wait the 15 months for termination of pregnancy +180 days before being able to take the APFT again. And even then she failed, due to complications (wripped stitches, infection, etc) with the cesarean section.
So, my best advice:
Have your wife speak with the commander using his open-door policy to discuss the issue. If he is not lenient in the slightest, then that issue is final and dead. Let it be.
Additionally, don't allow your wife to prescribe to the "I'm eating for two now" thought process. She needs to maintain as much physical activity as she is able to, and needs to eat healthy foods (large contingent of raw and/or steamed vegetables, turkey/chicken/tuna, red meat if necessary, avoid sweets and carbonated beverages).
The intent is that she stay in decent shape during her pregnancy so it is
possible to pass her APFT at 180 days postpartum. If she gained 80 pounds during the pregnancy (only 20-30 of which is actually from the child), then it isn't going to happen.
And good luck. I don't envy your (or her) position, although I am familiar with it.