You can't hold a work permit on a visa exempt entry, so that would be invalidated. Looks like you are maybe gonna have to start the whole process again.
OK, if you are still on an actual VISA, then that does not need cancelling. If you are on an extension of stay, that does need to be cancelled. You need to get a letter from your education provider stating your last day of classes, take that to immigration and cancel your extension, (this can be post dated). As for staying after the cancellation, you can buy a 7 day 'get out of the country' extension for 1900 baht.
Something dodgy going on. Plus, you won't get back to back Non-B from embassies, they are annotated with the company name, and after the first one, they will tell you to extend.
The reason people use a border run company is one, ease of travel and two, they will only take you if they are sure that you will be able to re-enter Thailand.