Christy,

Are you aware that your gggrandfather is listed as being a corporal with the Wilson-Gonzales'-Hughe's Battery ? I mean the NPSCWSS system lists him as enlisting as a corporal and mustering out as a corporal. His unit surrendered May 1865 with the 7th Texas Artillery Battalion. In the NPS CWSSSystem , he is listed as being on Film # M227 roll 22. I'll get back to you later on about the east Texas CSA website.
Let me tell you something about desertion in the War Between the States. Eventhough being convicted of being a deserter could have fatal consequences , the term was sometimes used rather loosely. There are plenty of documented stories of good Confederate men who , at one time or another , just walked away from the army to tend to some critical situation at home.Most of them either returned to their original units or joined another unit that was closer to their family .That could especially be true with your ancestor's outfit because they were a Trans-Mississippi unit who stayed on the west bank of the Miss. River . and served in Texas ,therefore , it would not be too difficult for him to get back to Texas.Also , if he did do something like this , he might have been under the command of an officer who did not like him or who was a strict disciplinarian (sp) and immediately marked him down as being a deserter when he did not show up for muster. That kind of thing ( just walkling off from their unit) happened all the time. Sure , some stragglers deserted from the army , but there are plenty of stories of men doing what I outlined above . It even happened in General Lee's famous Army of Northern Virginia. In fact , Lee understood this phenomenon and at least once , he factored it into how he planned a new campaign . That is , he understood that after a battle like Gettysburg , for example , that men would continue to show up in camp weeks after the battle . Some had been separated from the main army , some had been wounded , some were captured and later escaped , some ran away ,and some just went home after the battle to return to the army later on. People that don't believe this should read what General Longstreet said after Pickett's Charge failed .He knew that soldiers would gradually start returning to the army camps in the days and weeks following the horrific battle at Gettysburg.
Your ancestor may or may not have deserted , you may not ever know the circumstances ; however, I just wanted you to realize that in the War Between the States the term could mean a lot of things . Deserting your comrades in the face of the enemy is one thing, going back home to tend to a sick , starving or dying wife , child , parent or sibling is a different matter. Which is the higher calling ? Each man would have to answer that for themselves.
Let's see if we can find Lilley's Unit and some other information before we call your ancestor a deserter.
Regards, Craig Morin