Been doing some research and testing to update games backed up with BM, and thanks goes to AchillesPDX for telling this!
1. Download the Update to your PC using the PS3 Demo Manager proxy program or from the links provided here.
2. Use the PS3 Demo Installer to create the extra files you need to install on the PS3.
3. Using the instructions that come with PS3 Demo Installer, FTP your update to the PS3 using the FTP server.
4. Reboot without the jailbreak enabled and install the update.
5. Reboot again WITH the jailbreak enabled and start the FTP server.
6. Replace the EBOOT.BIN that got installed from the update with the decrypted one that originally came from the blu-ray disc. It should be located in dev_hdd0/game/(your games serial number)/USRDIR
7. Exit the FTP program.
8. Launch your backup.
And here is the deal, there was some question about 6. that maybe it would make the backup (not updated again since its original EBOOT.BIN), but i can confirm thats this is not the case.
Here´s what i did, backed up Resident Evil 5 and when i started it he tells me there is a new update availible in this case 2.0 (if you try to install it with the game running from BM it will give you an error after download complete and its going to install), so i rebooted ps3 and ran the game from the original game disc and he tells me there is an update and this time it will sucess installing.
Turn of ps3 and jailbreak it again, start FTP and replace the EBOOT.BIN in update folder with the original one /dev_hdd0/game/LAUN12345/GAMEZ/BLES00485/PS3_GAME/USRDIR , and this time when i start the game thru BM it wont say anything about a new update.
That makes me think atleast that the update is fine, as it doesent ask to update anymore.
If anyone has anything to add please tell me, im not certain it works on all games gonna try some more, biggest problem is to get hold of the update files when you dont have the original game disc, (i dont seem to find all newest updates on the psn file list on the site)
And really sorry if i write cryptic (hard to understand), not writing much in english let me know if its anything unclear and i try to explain!
Update: Same goes with Red Dead Redemption, to works after update to 1.04 (game data tells version: 1.04) and runs fine with backup mananger!