He has permission to shoot rabbits on the one and rabbits and deer on the other so if the landowner is not the holder of the shooting rights then he cannot give permission to anyone to shoot deer from his land even though the deer is on ground that he can shoot deer on.
If he shot a deer from this land and then the shooting rights owner turned up, in law, the onus would be on him to prove that he shot the deer whilst on the correct land as it could be suggested that he shot it on land which he didn't have permission to shoot deer on.
At the end of the day, it is far better to just do what you know for certain you can do rather than just do something because you think its correct as the law does not accept this as an excuse in court. You as the shooter will always have to prove you are right and not the law as they will accept third party evidence as factual.
Easiest thing to do is find somewhere to put a high seat up on the land where you do have permission to shoot deer or check who has the sporting rights for the other land and try to get an agreement in writing that they are ok with you shooting over their land to cull deer on a neighbouring land.
If land around you has stalkers on it you can guarantee you are being watched, waiting for you to make that one little mistake which you can be reported to the police for and with trail cameras everywhere they would have all the evidence they need.