When you change, AoBs, you basically edit the internal loaded memory that the flash file takes up on your computer. It's not detectable by Kongregate directly, though there is a chance that the (noob) hacker messes up the AoB and either a) breaks the program or b) the program is smart and detects the AoB change and reports it to Kongregate. Though I'm not sure if flash can do checksums on its internal memory space..... anyone?
By using something simple like tamperdata, you can see the communication with server, and see that the server is mainly just doing stayalive checks with the chat/login server. As far as I can tell, there's no active checks of data, thus any checks would have to be in flash.
Certain game makers add a value 2-3 times, if just one of them is changed, it checks against the others, and reports to the server. Also, certain game makers have a check based on how much you could have earned by that point, ie having 2 billion gold when most you could have earned is in the thousands.
Kong overall does not fully support games reporting hackers, in the event that some dick wants to program a game to detect your user name, and ban all the people he doesn't like. (its already proven you can import user name) So they take any reports of a user with a grain of salt....