If you have been through the Official Records you can see that they are fairly complete. One of the books my parents gave me is a register of Lee's dispatches, which are nearly day-to-day. Records destroyed must have been muster rolls, commissary reports and other records from the period 1864-65. Regimental adjutants forwarded copies of rolls to the War Department in Richmond, so that even when originals were destroyed, the War Department copy remained.
It took two-three years, but I have read through monthly inspection reports of Lee's Army of Northern Virginia which cover the period from August 1864 to February 1865. These are quite detailed, and include comments on each command at the brigade and regimental level written by brigade inspectors. Unless a command was transferred elsewhere, such as Butler's Cavalry Division, the same regiments and batteries are listed on every report. There is no mention of any slaves under arms because there weren't any.
The National Archives collection of Confederate records in Record Group 109 is so extensive that no one could go through them all in a lifetime. The records of Confederate citizens and businesses alone would overwhelm anyone thinking of reading all of them.
Another collection I have studied on microfilm includes letters written to the Confederate Secretary of War. These include correspondence of all kinds, such as a citizen from Mobile who wanted to organize water brigades to provide for soldiers on the march and on the battlefield. Most of the letters concern organization of new companies, battalions and regiments, some of which were authorized, while other offers were declined. I read every letter written from August 1861 through February 1862 - no offers for any black military commands.
I would have fallen out of my chair if I had found one. You can rest assured that I would have reproduced it word for word on the Message Board.
Offers of service are not evidence that such offers were accepted. For instance, letters to the Governor of Alabama include an offer of miitary service by little boys from a military school. They were no more than fourteen, some as young as eleven. The governor's secretary initialed and dated replies. This one had none, showing that it was simply filed and forgotten. I found no record that any of these little cadets formed their own military company.
The same is true for offers of military service by women and black people from a community. Governors of different states like Tennessee and Virginia received offers of service which were politely received but never acted upon. The patriotic gesture was sufficient. Accepting such an offer on face value and sending women or blacks into camp to organize and train for service would have been regarded as an insult to patriotic citizens. Southerners often say things to be gracious that they don't really mean. Example: the traditional farewell of a Southern visitor, "Ya'll come go with us," urged on the host a time or two, which he or she politely declines.
As a youngster I always wondered what might happen if we replied, "Okay - give us a minute to pack a suitcase with clothes for a few days."
Finding authentic evidence -- not someone's claim - of a Black Confederate military command in actual service would be like proving life existed on Mars. True believers don't really care about the evidence unless it supports their cause or can be construed to do so. If my personal feelings on this issue are in question, I don't care one way or another. If someone can produce an account by a Confederate officer or enlisted man who led one of these Black Confederate commands, I'd be happy to read it. If it's authentic, then count me among those who will support at least that claim.