The honorable discharges would not "trump" the dishonorable, unfortunately. A person may have served at different times, in different branches, or even the same branch, and receive multiple discharges.
Your court-martial conviction, sentence, and category of discharge stand, unless overturned by appeal by a military or civilian court.
Your time to appeal to a military court would have expired by now.
You may apply to the Department of the Army for relief...either upgrade of your discharge, or reinstatement of certain benefits. It will not be an easy battle.
If there are monetary benefits that you have been denied because of the discharge you received, you may also sue the Army in the US Court of Federal Claims.
The above being said, the likelihood of your success, unfortunately, is very low. The Army screwed up, and should not have allowed you to 're-enlist. Hopefully, they will see that they are at fault, honor your honorable portion of service, and do the right thing...even though not legally bound to do so.
Best of luck. I'm sorry you're in this predicament.