The only thing you have to remember is that when the battery is reconnected it will always return to the state it was in when disconnected. So if it was locked and immobilised when the battery was disconnected (as will happen if the battery goes flat), it will return in that state. The only time you will then have a problem is if the microswitches in the drivers door latch are poorly. As the battery has been disconnected the fob will no longer be synced and, with faulty microswitches you won't be able to enter the EKA. However, if you are disconnecting the battery deliberately, then it is pretty likely the car will be unlocked so the immobiliser will be off and that is how it will be when you reconnect the battery. You shouldn't even need to sync the fob.
When the late Orangebean first went into hospital, he emailed me asking if I could send an idiots guide to removing the battery on his VSE as he didn't want to deal with any problems when he came back to it (which he, unfortunately, never did). As this was going to be done by a non-technical friend, it had to be easy to follow so it's worth reposting here for anyone else who wants to do the same.
- Unlock the car using the remote fob and the central locking should unlock all the doors.
- Pull the bonnet release and open the bonnet.
- Close the car doors and lock the car using the key in the door (NOT the remote) but leaving the bonnet open. That alarm will beep and the dash display will show 'Bonnet Open'. Don't worry about that.
- Disconnect and remove the battery (negative off first).
- Close the bonnet so the car is now fully closed up and locked
- Connect the battery to the charger on maintenance setting.
When the time comes to put the battery back on,
- Unlock with the key in the door, only the drivers door will unlock.
- Open the bonnet.
- Close the car door and lock the drivers door with the key.
- Refit the battery (when you connect it you will hear the central locking motors try to lock the already locked doors). Positive on first.
- Unlock the car with the remote fob - IF it doesn't unlock on the fob (which it should), unlock with the key. As long as the central locking unlocks all the doors, everything is fine.