I think it's even more likely that the high command will leave the orders in place.
The "high command" may indeed leave the orders in place but the highest command, the CIC can and probably will stop it with a phone call.
Not that I wouldn't put it past him to do so, but Kellyanne Conway made a big deal on Fox this morning on how what happened to the Vindman's wasn't retaliation just a normal rotation of officers in and out of the NSC. If Trump personally decides on the orders for a lieutenant colonel then he'll make Conway out to be a liar and probably cost him among the military.