My AP went thru security to come back home last July and then to go to WDW in March this year. no problem.
Xrays don't involve any magnets. If they demagnatized your passes, they would also demagnatize all the other things you send thru that have magnetic strips - credit cards, driver's license, etc. As Debi mentioned, magnetic strips can demagnetize each other if they touch. Someone also posted that a magnetic catch on her purse demagnetized her cards.