In the normal course of things, your first stay should post first, because of timing. However, if the first one had a problem, and had to be posted after the second one for some reason (or was just plain slower), you'd have to explain the points you should've earned to Hilton, and I'd bet they'd make a manual addition of the difference for you. I can't recall whether it was Hilton (or more likely IHG) that this has come up, and it was resolved.