I would agree with challenge response,
Most devices i have played with have switched to a full hardware dongle, but before that there where ones where the plugged in tool would only present a single HID, the program would issue its first challenge, respond, and then the micro would challenge, pc respond and it would wake up, and keep on doing this each minute.
I know this because i ended up breaking the challenge / response so i could replace the software, but it was not easy because they where properly using the encryption functions of the micro they had. took a month of weekends. (developers had gone bust years ago)