Well, like I said, it is very confused.
I think that it is a strong possibility that the flag capture at Talledega is entirely fabricated!
Dupree was not with the 16th/12th at the end. His final records are found with the 6th Ala. Cav.
The 16th/12th is credited with being at Selma. I'm not positive, off the top of my head, but I think that the 1907 Census confirms that at least some members were there.
It is very clear from the research that I've done that the regiment was indeed split. It is a long and complicated story, which I won't go into [and its been awhile since I researched this, so its not fresh in my mind], but it revolved around a personal dispute between Armistead and Armstrong.
It is also clear from the evidence that Company D was never really a full fledged part of this regiment. It remained independent [documents signed until the end "Dupree's Independent Cavalry Company" and sometimes "Duprees Ind. Cav. Co. *attached* to the 16th Conf. Cav."], and sometimes served with the 6th Ala. Cav. instead of the 12th/16th. Company D is mainly what I have researched, but more research *might* show that the entire regiment was very loosely formed...even more so than the usual cavalry regiment.