No, it doesn't ask.
I thought of making it ask, but it is difficult to ask a meaningful question in 2x8 characters of LCD display.
I could have asked "Link Now?" or "Link to FS2?" or something like that, but that would likely confuse a customer even more than not asking.
It will only link if the file they are flashing has been "Saved for AutoCal" and has the tuner's FlashScan license number in it. They only window of opportunity for linking to the wrong license number would be if the customer tried to flash in a file from another tuner that had also been "Saved for AutoCal" instead of flashing in the file supplied by the tuner who sold them their AutoCal, which is unlikely to be done by accident. If the user tries to flash in any other file (that has not been "Saved for AutoCal") they will still get the "This file is not linked to any AutoCal device." error.
Regards
Paul