To clarify, there was nothing published by Jordan to substantiate his claim of 100,000 black confederates or 10,000 black confederate soldiers. Not sure I would include such unsubstantiated claims in the catagory of 'scholarly' or 'peer reviewed' either.
I don't recall any claims of a "cover up." Evidence? Pages?
I was assuming a familiarity with Jordan and his research on your part based on your positive comments of his work. One need only search on 'Elvin Jordan+ cover-up' to find an example of his oft-repeated claim that there was a conspiracy to white wash black involvement in the confederacy.
Show me where Jordan misused sources. I'll be at school tomorrow and can supply quotations. Can you?