Christy,

I may have found the problem. As you already know, Capt Lilley's Company joined up with W.H. Beazley's outfit . Beazley et al, shortly thereafter, joined Morgan's nine company Texas Cavalry Battalion as Company K. I believe this addition should have made it a full regiment. However, the force was never formally recognized by the CSA War Dept. Let me quote to you from " Texas in the War " by Wright and Simpson; " Fitzhugh ( early Texas CSA compiler) states that Morgan's Texas Cavalry Regiment was formed during March 1865 , by the addition of a tenth company to Morgan's nine company battalion. The names of the regimental officers were announced, but no formal muster was held as far as can be determined. According to Fitzhugh, this reiment was never fully recognized by the Confederacy; and the three officers involved were never promoted to their regimental ranks".
Sifakis lists Morgan's "Regiment" as existing from March - May 1865 and being under the command of Parson's Brigade ; Steele's Division ; Wharton's Cavalry Corps ; Trans Mississippi Dept.
Sifakis suggests for "further reading" , " Between the Enemy and Texas : Parson's Texas Cavalry in the Civil War" by Anne J. Bailey .
Morgan's "Regiment" was surrendered by General Edmund Kirby Smith , commanding Trans Miss. Dept on May 26, 1865.
Based on what I'm seeing in the literature, it looks like Morgan's Cavalry Battalion was formed and "recognized" ( by CSA War Dept) in 1863 and participated in some of Gen Marmaduke's Trans - Miss. operations , however, when the 10th Company joined the Battalion , it was never recognized as such ( as a regiment) and as a result, the records of the Company K
were , evidently , never made an official part of "the record" . Also remember the time when all this was happening , Lee was only a few weeks away from Appomattox and Richmond was in chaos as the Confederacy and its governmental infrastructure was dissolving.
So, once again, not to sound corny or overly sentimental about Capt Lilley's last days in the Confederacy, but the best document you may come up with as a vindication of his good name and his military service is that W.H. Beazley vouched for Lilley's military service as justification for his widow to receive a CSA pension. Believe me , as high as post war feelings and emotions ran in "Reconstruction Texas" , I just can't see the State of Texas agreeing to award a pension to the widow of a man that Beazley considered a bona fide deserter. Beazley could have easily given a "thumbs down" to the request and he did not.
Christy, I think you're running up against a problem with the timing of Lilley's and Beazley's joining of Morgan .My guess is it was just too close to the end of hostilities to get very much into the record.
I consider other visitors to this site to be much more expert on these matters than myself. I am an amateur. Perhaps Jim Martin or Hayes Lowe or Thomas Reid could shed some more light on this.
Best of luck and best regards, Craig