I believe the John mentioned was either Henry's brother, John, or as you said his father. Sounds like he preferred to stay with the Army of Tennessee rather than return to the Army of Northern Virginia.
I am still surprised that in all of the write-ups on the web sites, there is no mention of Chickamauga.
I also have the problem of Henry Travis listing his captain as G. F. Foster of the 11th Texas Vols.
He said that he had passed through Osyka, Mississippi on the way to Virginia as did the 4th Texas, but did not mention the 4th Tx. I wish I could get someone to find out more about Capt. Foster and the 11th Texas Vols.