Got an unsatisfying answer from Telltale:
I apologize for the problem you are experiencing. We are aware of this issue, and currently investigating a potential solution. Unfortunately, once the saves are dissociated from your prefs file, they will no longer appear on the in-game save screen. This can occur when saves are corrupted or when they are manually reset by holding the spacebar while launching the game. The only recourse is to replay episodes 1 and 2 or play episode 3 with randomly generated choices.
I guess it's not a big deal to replay them, but I'm going to wait until all five episodes are out. I don't want to risk this same bug every single time a new episode comes out. Grrr...