This response is provided based on the information you shared and should not be used as the sole source for making a decision. You should seek guidance from the chain of command, IG, JAG or other certified agencies before making any decisions. How you chose to use this information is totally up to you and is your sole responsibility.
It depends on when the Soldier became pregnant as determined by medical authority. Specifically the AR states:
In the case of a pregnant Soldier, if a physician determines that the Soldier became pregnant prior to being entered into the ABCP, the commander will close the Flag using codes KZ, not KE. If the Flag was initiated before pregnancy (as determined by her physician) the Flag will remain in effect until the Soldier complies with AR 600–9. Remove the Flag (code E) on date of compliance.
AR 600-8-2 paragraph 2-3c states:
Flag code K “Noncompliance with Army Body Composition Program.” The effective date of the Flag is the date that the Soldier was found to be in noncompliance with AR 600–9. The use of certain medication to treat an underlying medical disorder or the inability to perform all aerobic events may contribute to weight gain but are not considered sufficient justification for noncompliance with AR 600–9 and the Soldier will be flagged. Soldiers will not be exempt because of chronic medical conditions unless an exception to enrollment in the ABCP is granted by the DCS, G–1. In the case of a pregnant Soldier, if a physician determines that the Soldier became pregnant prior to being entered into the ABCP, the commander will close the Flag using codes KZ, not KE. If the Flag was initiated before pregnancy (as determined by her physician) the Flag will remain in effect until the Soldier complies with AR 600–9. Remove the Flag (code E) on date of compliance.
Hope this helps to some degree.
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