Reference regarding Amphibious Assault: AAE40 page 15 Section: Transports, second and third paragraph:
"A transport can land units while in any friendly sea zone along its route, including the sea zone it started in. If a transport loads land units during the Combat Move phase, it must offload those units to attack a hostile territory as part of an amphibious assault during the Conduct Combat phase, or it must retreat during the sea combat step of the amphibious assault sequence while attempting to do so. A transport that is part of an amphibious assault must end its movement in a friendly sea zone (or one that could become friendly as result of sea combat) from which it can conduct the assault.
Any land units aboard a transport are considered cargo until they offload. Cargo can’t take part in sea combat and is destroyed if the transport is destroyed."
Based on the above text, loading the transport during combat means the units must be unloaded during combat, and if not unloaded during combat are treated as cargo since unloading a transport is part of the transport’s move and the transport’s move has ended during the combat phase as a result of the amphibious assault. Also, it clearly states that units loaded during combat must be offloaded in a hostile territory and a friendly territory after the retreat would not be a hostile territory for unloading.
Furthermore, with the exception of air units, no sea or land unit moves in both Combat and Non Combat phases, therefor it is logical to assume they are stuck on a retreated transport until their next turn, in which they may be moved during either phase as normal.
Well, that is my best guess anyway. I am not affiliated with the game so this is not an official answer. I hope this helps.