All of this is straight out of TC 3-22.20. Based on the information that you provided, I don't think the flag is valid. You need to bring this up to your immediate supervisor. If they are not willing to help, go the the next person in your chain of command.
RECOVERY FROM INJURY, ILLNESS, OR MEDICAL CONDITION
6-6. Soldiers recovering from injury, illness, or other medical conditions must train within the limits of their medical profiles (DA Form 3349 [Physical Profile]) and be afforded a minimum train-up period of twice the length of the profile. Prescribed train-up periods must not exceed 90 days before APFT administration or other unit physical readiness goal requirements IAW AR 350-1.
PROFILES AND RECOVERY PERIODS
6-30. Soldiers in the reconditioning program will be on a physical profile or in the authorized recovery period from a temporary profile. Commanders may assign Soldiers with a permanent profile to the reconditioning program or allow them to remain in unit PRT. Soldiers on convalescence leave may be exempted from reconditioning at the discretion of the profiling medical officer. In no case can a Soldier carry a temporary profile that has been extended for more than 12 months without positive action taken to correct the problem or effect other appropriate disposition IAW a military medical review board. Once a profile is lifted, the Soldier must be given twice the time of the temporary profile (but not more than 90 days) to train for the APFT. It is not a requirement to take an APFT after the recovery period if a Soldier is not due to take the semi-annual test. Refer to AR 350-1 and Appendix A of this TC for APFT policy and procedures. The RPL follows the medical guidance on the profile for Soldiers on profile. If there are any questions about the limitations of the profile, the RPL will contact the medical officer for clarification. Once a profile has expired, Soldiers will remain in the reconditioning program until they have met transition criteria to return to unit PRT activities. During this period, the RPL/ARPL, and unit reconditioning NCOs will reinforce the precise execution of PRT activities with each Soldier in small groups or individually. See Figures 6-2 and 6-3 for transition criteria to move from level I to level II or return to unit PRT.
A-41. Soldiers with temporary physical profiles must take a regular three event APFT after the profile has expired. Soldiers with temporary profiles of long duration (more than three months) may take an alternate aerobic event as determined by the commander with input from health-care personnel. Once the profile has been lifted, the Soldier must be given twice the length of the profile (not to exceed 90 days) to train for the regular three event APFT. If a regularly scheduled APFT occurs during the profile period, the Soldier should be given a mandatory make-up date for the APFT.