While being ferried on the Shuttle Carrier Aircraft, were the shuttle orbiter's control surfaces (rudder and elevons) adjusted by controls in the SCA, to assist maneuvers? (They were, after all, fly-by-wire.) Or were the control surfaces simply locked in a neutral position?
For the Orbiter aerosurfaces to move, hydraulic pressure must be supplied from the Orbiter's Auxiliary Power Units (APUs) (a poor name for these critical devices - the name came from the analogous devices in aircraft!).
The APUs were not running for ferry flight, and control locks were installed to hold the elevons in a neutral position.
For the ferry flight configuration, the tail cone fairing is installed on the orbiter to decrease aerodynamic drag and buffet, and aerosurface control locks are added to the orbiter's elevons. The orbiter is unmanned and the orbiter systems inert.