VFS Global is a highly reputable company based in Bangkok and Chaing Mai. They are not un the habit of loosing documents. I have used them for obtaining a new UK passport and their service was excellent.
If it's any help you dont need passport to do 90 day report and you can board domestic flight using Thai driving license if you have one. Might help you get to Bangkok to do application for new passport through VFS Global. I'm assuming you are British?