This is one of several problems relating to control in the sense of 'this region is occupied by a large number of our guys' versus long-term control in the sense that the bureaucrats, minor nobility, and tax collectors now answer to realm B instead of realm A.
The former is achievable by winning a battle and clearing out enough of the enemy. If you are in a position to begin a takeover, you 'control' the region - certainly you control it more than the local lord whose garrison was just defeated.
The idea that five hundred troops could spend a week working on the local infrastructure and other takeover activities and then suddenly the local lord who hasn't been in power for that whole week can up and convert everything to another realm and single-handedly un-do the work of the armed soldiers occupying his region is pretty absurd.
Just because realm B doesn't yet fully control a region does not mean that realm A still does control it.
