First and foremost, a warning — at this current time it is advised that you stay offline and avoid playing any AP2.5/XGD3 backups. It has been confirmed by the team that the dae.bin is now being silently updated on all LIVE-connected boxes.
This update is not being deployed via a SystemUpdate or TitleUpdate, but rather occurs in the background without any visual indication or prompt to the user. As such, there is no means by which it can be cancelled or avoided, other than not connecting to LIVE. If you've connected to LIVE in the past 24 hours, your system has likely already been updated with a changed dae.bin.
All AP2.5/XGD3 backups that contain the now older AP25 replay data will fail the system's AP2.5 challenges and indeed flag your system (the flagging has also been confirmed by the team).
Like our news a few days ago, the dae.bin is now being changed by way of an appended challenge table in the same manner on current retail dashes (13604) as it is on the preview dash (14686), however the content of the challenge tables differ. The team has determined that the appended challenge table appears to be unique per console and contains indentifying information. This means that everyone's dae.bin is different, and can potentially be traced back to your specific console. Therefore, sharing your dae.bin with others is not advisable.
More info to come.