Technically, we can argue that the tank commander resumes his reload inside the turret as he is invisible, but this just seems like a bug as there can be other positions with FFV which are not capable of doing so, like the MH-9 Co-pilot and are visible.
My suggestion is that the moment FFV is disabled, any reloads in progress are aborted.
To really drive the point home, as co-pilot start flying the helicopter, release controls, start reloading your rifle and take controls again.