You say your son was Sailor of the Year at his current Command. That tells me he has friends in high places. What your son should do is have a private talk with his LPO and ask him/her for advice. This will effectively let the Chain of Command know that there's a problem. That's his first step.
If your son doesn't feel comfortable talking to his LPO he should set up a private meeting with his Chief and invite the LPO along so he's not left out of the loop.
And keep us posted on any developments.