Originally Posted by
findark
The scanner would certainly have beeped, but it makes the same beep for any number of reasons (boarding out of order, exit row assignment, etc.) so it's not implausible that the agent ignored it.
Especially possible given that the OP stated that he was sitting in the exit row.
Also if there's a problem with scanning the BP then they will normally just enter the sequence number printed on it, which will not trigger the beep as it's the same even after an upgrade.