Final update for the night. Trying to keep the posts separate instead of amending the original to make this easier to read. Doesn't seem like this specific forum gets much daily traffic anyways.
Cleared system cache - no change.
Generated new save file by changing storage device and then loaded into co-op menu. There was a longer hesitation than normal as it appeared to download my stats. Unfortunately, the stats it downloaded were the ones from only my previous game.
For now I'm going to leave it, come back in a day or two and hope to some furry god that they get restored.
Honestly though, I have a strong feeling they were overridden on EA's server. Makes me feel better about not playing any of their other EA multiplayer games like Battlefield. Not sure I could stand to lose all that progress all over. Then again, I still have Mass Effect 3 on the horizon.
Cheevos are a hard mistress.