You would have to 'mark' the items the soldiers brought with them or devise another belonging rule if you don't simply return everything to their homebase straight away. Otherwise even your flares would show up on the mop up transfer list.
Since I am daydreaming anyway, how about missions taking their time on the geoscape, i.e. having the skyranger landed and unavailable for a certain period of time, depending on how many turns the battle took? If that was implemented you could create an option like "collect all carryable stuff into the skyranger" at the end of mission, binding it for another few hours or so.
