Thank you for all your replies, it really has upset the family, its amazing how much you become attached!

In answer to your questions, yes she is chipped. I have looked in the local vet store and have not seen chip catflaps? are these available in the U.K and how do you set it? This would solve the problem outright.

We could lock her in at night and use a litter tray as she was very good with these when young, but during the day the evil tom can still get in.

Good idea about clear varnish but its not just the magnet, its the whole trauma of having a collar on that freaks her out.

My wife thinks the Tom is a stray as he is very dirty and is constantly walking round shouting as if he is hungry, we have not fed him as it will be the end. We are thinking of giving the local cat protection league a call to come and 'pick him up' but how do you know 100% that it is a stray and not just horrible owners that don't care?