I WAS JUST CURIOUS TO SEE IF ANYONE KNEW THE REGULATION THAT STATES A SOLDIER WHO HASN'T TAKEN A RECORD APFT IN 12 MONTHS IS FLAGGED FOR BEING OUT OF TOLERANCE. I NEED TO KNOW IF THERE IS AN EXCEPTION TO THE REGULATION. FOR EXAMPLE, IF A SOLDIER IS UNABLE TO TAKE THE APFT BECAUSE OF TWO SURGERIES ON THEIR ARM IN THE COURSE OF A YEAR. THEREFORE, LIMITING THEIR ABILITY TO TAKE A RECORD APFT. IS THERE ROOM FOR AN EXCEPTION? AND IF THERE IS, IS IT IN WRITING SOMEWHERE?

Check out AR 600-8-2 it's the Reg for the Suspension of Favorable Personnel Actions.

AR 600-8-2 States some of the following:
1–13. Circumstances requiring a transferable flag
The specific actions and investigations listed below require a transferable flag.
a. HQDA directed reassignment of flagged soldier. Remove the flag according to HQDA guidance.
b. Movement of an adverse action into the punishment phase. Remove the flag according to the rules in paragraph
1–12a.
c. Failure to pass the Army Physical Fitness Test (APFT) or failure to take the APFT within the required period. Remove the flag (code E/type report) on the day the soldier passes the APFT or at expiration term of service (ETS)/expiration of service agreement (ESA)/mandatory release date (MRD).

I was unable to find what they define as the required period, but I'm believe its one year. It also goes on to say:
1–15. Processing exceptions
a. APFT.
(1) Flags for APFT failure block promotion, reenlistment, and extension only.
(2) A flag is not initiated if the soldier has a limiting physical profile that specifically prohibits taking the APFT.

That should be what you're looking for.

You do realize that if the Soldier is on profile b/c of those surgeries, then s/he cannot take the PT test therefore s/he cannot get flagged...now if the Soldier just decided they werent going to take one then yes that could cause a flag...