Hanks was present because this was to be Rudd's 5th time hosting, thus his induction into the "5-Timer's Club", and Hanks would have been part of that sketch. As to why he still appeared, he answered that during the open: "You think I'm going to fly 3,000 miles and NOT be on TV?"
I'm not sure why Charli XCX is said to have "bailed out". The show, as aired, clearly ran with a less-than-skeleton crew (from what I could tell, there were MAYBE two camera operators based on the rigidity of the home base segments, and I'm guessing few-to-no stagehands, given that they didn't bother to bring in the Update set). It's likely her band, roadies, etc. would have exceeded the limitations placed on production for that evening, so her performances were scrapped.
Was it a great episode, even by SNL standards? No. But given the situation, they did the best they could on short notice - and I still think this was preferable to putting on a proper rerun, as at least some new material got to air.