There is no such policy. There is no AR that limits a commander's ability to accomplish his or her mission.
So whomever told you of this policy was mistaken
It sounds plausible...that is, it makes some sense that after a soldier
has completed his physical you do not want to take a chance of injury. But the fact is that a soldier can be issued any legal order, including orders to train, work, heck, you could be ordered into combat (if you were in theater) despite the fact you went through the physical.
If you were injured, you would be able to either
1. Request for the physical to be ammended based on the injury
or (more common)
2. Go to the VA and they can provide treatment and compensation for any injury in service
I am very sorry to have to bear bad news.