@Snoangel26, I've spent the entire day today reading through your dad's thread here. It's heartbreaking, but your perseverance is inspirational.
Reference the SSN that you got off a military document, it may be possible that it contained a typo or that the PI firm that ran it for you and advised it was 'in use by someone alive' may have typoed in their own search.
I say this because you've stated that the detective you've been in contact with knows your dad's SSN and has advised that your dad's SSN has not been used (in years at least) and that would directly contradict what this PI firm stated. I'd trust a detective above a PI firm at this point.
Might I suggest that your most economical means of 'verifying' would be to email the detective once again. Let him know that you received a military record for your dad with SSN #### on it (let him/her know what that number you got is), and that you had it run by a 3rd party who advised you it was in use by a living individual.
That detective is either going to come back and tell you that the number you have is wrong or is going to dive into WHY another individual is utilizing your dad's assigned number. It would certainly be relevent to that detective in your Dad's Missing Person Investigation.
Just my suggestion from afar. I wish you peace, success and hope in finding out answers.