Just out of curiosity. If I decide to update my PS3 now again, and don't use the jailbreak anymore, will I keep the trophies I got with game copies, or do they get lost? Or does Sony see that you got them with non original games?
Trophies will be kept during FW update and once you'll since them online they'll reflect on your PSN profile. And - so far I believe Sony has no tool in place to recognize which trophies were obtained from original and which from "backed up" games. However - they might be able to detect use of JB device even when your PS3 will be no more in JB mode or with JB device attached and after deleting the Backup Manager, any homebrew or all backed up games from internal hard drive.