Hi @FireDragonFlame,
Trophies are linked to your PSN ID, you can't delete them once they're unlocked. Most likely you're logged under a different profile and the game tries to access your existing game save data.
Make sure to use the profile you used to unlock the trophies.
Simply sync your trophies again in this case. I'm not a PS3 user so I'll refer you to their forums directly : How do I Sync Trophies on my PlayStation 3?
Alternatively some privacy settings can also leave the players under the impression that they lost their trophies : Lost my trophies?
Hope that helps.
