First off, I'm on 360 so this my not apply.
I did a post in the pinned bugs/glitch section with regards to local coop trading.
1. The why: even though you're playing local coop, it requires you to be connected to the net to trade; and it saves during all trades. Hence if your net cuts out during trading you get hit with the "your saved game has been manipulated"
2. from my experience this affects all your saved games/characters once it has happened.
3. the fix on the 360 is to move your profile or "gamertag" to a memory card, then back to the hard drive; or to simpy re-download your gamertag from xblive... as in recover gamertag. The fix had nothing to do with moving saved game data; only your gamertag.
Not sure how this would apply to the PS3 because I don't own one, but hopefully it's a simular solution. Good luck^^