Hmm, the only thing I could think of is if you transferred your saves from a much older version of the game, like version 0.4 or 0.5 and earlier. You'd have to restart if that is the case, otherwise I'll keep looking at it.
I did, yes. I didn't restart since the warning made it seem like the only risk was missing content from much later than I was. Alrighty, if that's all the issue is I can restart easily enough. Thank you.