A friend had to upgrade her cat flap a few years ago for exactly the same reasons but the intruders upset her two so much they started toilet scent marking! She gets all sorts of metal presents from her two - screws, wire, nuts & bolts. She had a problem initially with her nervous female cat not being able to operate the flap but resolved it by putting a block of wood outside to act as a cat step so the magnet operated the door more easily. I know, it sounds eccentric to me too! But it worked. However, don't wait too long to change the flap because her cats still aren't convinced that they're totally safe 2 years after the change. We think it's because the 'intruding' went on for years too.
Also she keeps a couple of spare collars plus magnetic tags so that if either loses a collar or magnet she can replace immediately.