Soldier failed AFPT can pass ACFT but commander states Soldier must take the APFT? Help!

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This appears to be a catch 22. The APFT is no longer (according to our understanding), valid as a test. However, the ACFT is not currently being used to validate fitness. Therefore I would suggest that this is a common sense leadership issue about doing what is right for the Soldier. Have the Soldier take one or the other and remove the flag. I would think the ACFT would be the proper course of action since the SMA wants as many Soldiers as possible to take the test to collect data.