Doyle, you are correct. Neither the company orderly sergeant nor the regimental adjutant could have kept track of the men left behind in Arkansas. Although I haven't seen the muster rolls of the 6th Texas, I have examined the muster rolls of other regiments captured at Arkansas Post and exchanged in Virginia. In all of the rolls I've transcribed, the men who had been left behind on detached duty, in hospital, or on furlough, were carried on the rolls in their last known status. At some point, normally on the April 1864 or August 1864 rolls, those men who had been on furlough when Arkansas Post fell were reported as absent without leave, and dropped from the rolls. Those men who had been left behind sick were typically dropped from the rolls for being absent without leave or "supposed to be dead", depending on how sick the soldier had been when last heard from before the capture of Arkansas Post. Those men who had been detailed on detached duty were normally not dropped from the rolls, but were retained as "absent on detached duty." Occasionally, word of the man's status might be received from a soldier who was returning to the regiment from furlough, if that soldier had happened to run into him or his family back in the TMD. In that case, the man's muster roll entry would reflect that information.

The Confederate Army didn't have a system for tracking the status of a soldier, apart from the regimental muster rolls. The regiment reported a soldier's status to the War Department on the muster roll, but the War Department had no official means of informing the regiment where its wayward boys were, except in the case of discharge or retirement to the Invalid Corps -- in those cases, a copy of the discharge or retirement certificate was sent to the regiment.

The field army, division, and brigade to which the regiment belonged could keep the regiment informed about a soldier's status (detailed, court-martialed, etc.) via copies of Special Orders; however, a regiment serving in one geographical department normally did not receive copies of Special Orders issued by another geographical department, even if those orders concerned one of the regiment's men.

In the case of men from the Arkansas Post regiments who had been detached as gunsmiths, armorers, artificers or mechanics at the Little Rock Arsenal when their regiments were captured, most, if not all of them had been transferred before Little Rock fell to the Yankees. As Little Rock became more exposed with each advance of Federal troops, the TMD began drawing down the personnel of the Arsenal well before the city fell. Most of them were first sent to the ordnance depot at Arkadelphia, then to Washington (Arkansas), and finally to Marshall, Texas (a few ended up at Tyler and other points in Texas).

If there is no Union POW record for Bill's ancestor, then he either followed the C.S. ordnance department's migration south, or had already left the service through discharge, desertion or death.

So you are correct in advising him that all references to his ancestor on the muster rolls dated after the capture of Arkansas Post are simply "when last heard from" entries. The regiment had no idea of where he was.