Microchip and cat flap problem

[SpanielPlusToddler]

I’m hoping for some advice or ideas that we haven’t thought of with our cat problem, thanks.
We have 2 cats, sisters, who are 18 months old. We got them spayed and chipped as soon as they were old enough. We have a sureflap microchip cat flap and they come and go as they please day and night. We live rurally so they toilet outside and have no indoor litter tray.
6 months after they were chipped one of them suddenly couldn’t use the cat flap, because it wouldn’t open for her. We knew the cat flap was working because it was fine with the other cat. We took her to the vet who first scanned and then xrayed her and said the chip had completely disappeared! Vet had never seen this before, but rechipped her.
No problems for another 6 months and then the other night we thought she had a tick. There was a strange lump, but not a tick. Took her to vets and it was her second chip emerging from under her skin! Vet has never heard of this before and said her body is rejecting the chip.
Meantime we took the batteries out of the cat flap so she can come and go. But the last few nights another cat has been coming in a spraying in our kitchen and utility room, eating their food and frightening them.
So, we don’t know what to do. Chipping again is going to keep coming out and hurting her. But can’t have other cat coming in and spraying, it’s so disgusting.

Please help any ideas? Thanks

[Polkadotdelight]

Does she wear a collar? If she does you could attach a chop to the collar?

[SpanielPlusToddler]

Thank you for replying. She did briefly wear a collar, but hated it and lost it outside within a day or 2. Might be worth trying that again though.