It's highly unlikely she has a re-entry permit as a DTV is a multi entry visa. Does she have a photo or scan of the data page of her old/stolen passport? That along with her new passport and a printout of the evisa should be all she needs to return to Thailand
Previously you could get a 1 year multiple entry extension based on marriage that gave you 90 days every time you entered Thailand but since the move to the evisa system this is no longer available. A single entry 90 day Non-O visa is all that is available now, and you can then extend that for 12 months inside Thailand. But you have to time that well, combined with re-entry permits to get this to work if you are in and out frequently
Of course they could, nobody knows what information you are supplying. But if you get all your personal information correct they won't cancel it again, though they may still reject at the next stage
In what way do you have a company in Thailand? You can't even be a director of a Thai company on a DTV far less do any work for it. At best you can be a minority shareholder.