I doubt very much Confederate records were ordered destroyed by order. Instead, they somehow were lost. Most of those sent to Richmond were destroyed when the city was burned.
Additionally, many Confederate soldiers filed application requests where they were then residing, not in the state from which they served. Also, the soldiers themselves had no records they could have saved other than parole or furlough papers.
In many cases, the State Pension Board, wrote the War Department in Washington, DC to validate a man's service. If this were the case with your ancestor it would appear on one of his cards found in his Compiled Service Record with a notation on whether or not his service could be validated.