yes they will carry over, but you'd have to sync every single trophy to your new system
killerband55
What he said. Trophies are stored on your PS3 system user until you manually sync them to your PSN user. Then the synced trophies are stored on PSN and can be accessed from any PS3 with your username and password.
If you are transfering data to the new Playstation make sure sync your trophies first before doing this and also follow the step by step instructionswith the data transfer. If you got trophies and then didn't sync them but transfer data over, those trophies are gone. You cannot get them again.
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