In this thread
http://club.cdfreaks.com/showthread.php?s=&threadid=55007&highlight=bg2 it says that the new BG2 executable is embedded with a new Securom version -- Baldur's Gate II (BG2) v4.82.00.0139. However, the messages above imply that the CDs do not contain any form of protection at all.
Therefore, the only thing I can guess that could cause the backup disc to fail is that the new Securom executable would be able to identify the "back-up copy" of BG2 as a CDR/RW media. Now disabling the ATIP-check (enabling Hide CDR-Media option of CloneCD) would solve the "copy protection" of BG2, unless the new Securom version (executable only, not the CD itself) would blacklist CloneCD's Hide CDR Media feature rendering the game not playable if this feature is turned on.
Now this can of course also be circumvented if you're reading the backup CDR/RW media from a CDROM drive that doesn't recognize the difference between a pressed CD and a recordable CD.
Has anyone actually tested that his backup BG2 CDs don't work when he downloaded the latest BG2 executable update?