She is still here. Her extension expires on december 26th. I would try to let her do a border run before 26th. But probably she will receive just a 30 day visa exempt (that, by the way, in Satun is not free for back-to-back travellers)
But now cannot fix the mistake at Immigration, she must do a border run and when re-enter show her "clean" visa and get 60 days. But in Satun they would not give, I asked already 😏
Visa sticker of course remain on old passport, but Immigration makes a stamp on new passport confirming you have a valid multi entry visa. And it is recommended to travel with both passports till when the visa is valid
Your Embassy will give you a letter to transfer your visa on new passport. With that letter and both passports, go to Immigration office (fee 500 baht). No problem on your work permit