You may be right, but I think a court martial is a matter of public record. It wouldn't be confined to just his personnel file. Furthermore, a court martial involves a lot of people and I would have to assume that by now one of them would have popped up either during his senate campaigns or more recently.
There is one possibility. I know from working at the Stockade at Ft Riley Kansas for a couple of months back in 71 that enlisted men were often given the choice of a court martial or accepting a less than honorable discharge. I doubt they would do that to a commissioned officer and I think the rules about discharges, etc are or were different for officers than for enlisted men.
I just find it very hard to believe Kerry could cover up a court martial and bad discharge. It's not out of the realm of possibility, but I very much doubt it is true.
Commissioned officers were given a chance to resign, I tried to put a lLT in jail one time.