I don't know what happened. Maybe the pip was underneath where you couldn't see it. Maybe the chick had crawled up under Mama's wing where you could not see it before.
If the chick absorbs the yolk and is is acting OK I'd try putting it back under the hen tonight after dark. It's challenging to raise a single chick and I think there is a pretty good chance she will accept it if it is healthy. Be out there first thing n the morning and check on how it is going. If she rejects it take all the chicks to raise together. That might even keep her on the nest long enough to hatch more eggs.
Good luck!