There are some armies (Marian Roman comes to mind) which allow you to purchase TF for the express purpose of protecting artillery. The rules (page 11) specifically exclude such TF from limits on the deployment of TF generally.
The Initial Deployment rules on page 22 talk about fortifications being part of commands and thus subject to the deployment rectangles.
Together, these rules suggest to me that if you have TF in your army, and also a Brilliant General who uses a Change Deployment stratagem, then the fortifications attached to a command get moved when the two commands swap places.
Assuming that's true, then would it always apply to all fortifications and obstacles? Or would it be possible to deploy some fortifications in front of troops during deployment, then leave the fortifications in place while swapping the troops behind it with those of another command?
Or, alternatively, is there such a thing as fortifications which are not attached to a command? For example, say I have Marian Romans commanded by Julius Caesar. I take Aeduan allies and downgrade the Foot Warriors to Hd (O) - not much good in the open but serviceable behind TF. I initially deploy them in a defile behind some TF, only to find out my opponent is planning to attack up that defile with, say, massed Wb (O). So I use my Change Deployment stratagem to swap the Aeduans out to an unthreatened flank and replace them with a command full of Ax (S) and Bd (O). Can I leave the TF in that defile for the Ax and Bd to defend, or does it get uprooted along with the Aeduans?