I was doing exactly the same 6 and 7 years ago so I believe the only thing that has change is the appointment system now whereas before you just rocked up and hoped the queue wasn't too long.
You need a TM30. Where are you staying in Pai? Ask at your lodgings/hotel for a copy of the TM30 they should have filed as it's their responsibility to register any staying guests.
Your current visa exempt stamp is void as soon as you stamp out through immigration regardless how many days are left on it but you can easily get a new visa exempt stamp when you come back to Thailand.
... the ME only gives you 90 days in country per visit. I used them for years as it suited my work rotation but now I'm on 2nd year extension of stay from a 90 day SE non O. The RE permit is easy, much easier than ME visa unless you know you will be FIFO on a regular basis.
I'm guessing he has a 12 month extension of stay based on having a Thai spouse in which case he needs to get a re-entry permit and follow the guidelines as per Ellie's post. If he does actually have a 12 month "marriage" visa, it will already be a multi entry allowing 90 days per entry and he can come and go as he pleases, respecting the 90 day max stay, without the re-entry permit but still needs to fullfil the covid entry reqirements.
... I've had one for years but my wife is still the house owner and although it helps as my registered address, buying cars, motorbikes etc, it makes no difference for submitting a TM30.