Did you ever figure this out? Because I’ve been having the same problem. I thought it was only when the numbered list had a character style applied to it but that doesn’t seem to be the case. I’m trying to figure out if there is a setting somewhere that put it on the other layer, but even so, it should just be hidden, not deleted entirely (which is what is happening). So far I’ve just been converting the numbered lists to text at the last minute but I’d rather not have to do that!