A year ago I was reduced in rank and recommended for separation from the Navy due to allegations of drug use. The allegations were completely false and I appealed my case at an Administrative Separation Board. The board found 3-0 that I was not guilty. At this point I submitted a correction of naval records to Navy BCNR to receive my half month pay x2 and rank back. 7 months later I received a letter from BCNR stating that there is no record of NJP in my Official Military Personnel File. I checked my official online records and what paperwork records I was given before the big changeover to digital and no documentation was submitted. I am not guilty and there is no record of this in my file, does anyone have any idea what I should do?

You refer to your rank so I assume you were/are a Navy Officer. Enlisted personnel have ratings instead of rank- that was the procedure when I was in the Navy anyhow. But that was a long time ago.
Is it possible that the Captain's Mast was expunged from the record after the Board made a ruling? Also, are you presently in the Navy?
And I think that it would be helpful if you would explain some of the terms and abbreviations you have used in your question.
You say that there is no record that you were found not guilty. Is there a record that you were charged?