Regarding Sandro's comment that transfer was "stateless" - all missions have timers that run in real time....
This is what I've been thinking about but felt like I was missing something critical and would sound stupid bringing it up. If there are technical limitations to having your ship disappear off the grid and appear again sometime later, then as far as the coding goes sure instantly transfer the ship - but add a lockout timer that says "IN TRANSIT" or some such.