Typically this is an easy process. When I worked at HRC and Soldiers would contact us about these issues we would refer them to the schools branch (usually this was for TDY enroute on a PCS). The school branch would document the issue and then reassign the Soldier to another class date.
If you are TDY and return to your unit there should be an OML. If should be rather easy for your leadership to use the medical documentation to remove you from the OML and send the next person on the list. Just make sure they reschedule you as soon as possible.
Another option is to contact the school house and explain your situation and ask them what actions are required for you to either attend with a profile or get rescheduled for the next class.
The last option might be that you can show up to school with a profile that allows you to take an alternate event. This could be an issue because you need 90 days to practice the alternate event before you can take a record APFT. See AR 350-1 for details about the APFT test and Schooling requirements.
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