The federal authorities can pretend to push around any paper they like for propaganda purposes, but the history of Texas is that the Confederate troops just went home -- on June 20-21, 1865, mostly without orders. They just decamped from their principal stations and rode home. With their weapons. Except for Jo Shelby and (I think) Kirby Smith, who went to Mexico instead, Shelby's troops in formation and with their colors, which they sank in the Rio Grande so as not to give offense to Mexico.
The People went home.
Kirby Smith surrendered the Trans-Mississippi Department on May 26, 1865 under the same conditions afforded the other capitulating generals. The soldiers were parolled and allowed to return to their homes in peace so long as they abided by their paroles.
The People were allowed to go home.
Right....:)
That is why the Yankees were so hateful to Texas during Reconstruction. Texas was NEVER conquered.