OK, that was weird...
I guess it's being sorted, my Carrier-owning alt has successfully jumped. Meanwhile the Carrier my main is riding on has also jumped... but for awhile it was in two places at once. Carrier Management said it had jumped and was preparing to jump again, but my CMDR was still at the original location, and still on the Carrier.
Curious, I clicked on "return to surface", wondering if that would update something, but all indications said I was still in the system the Carrier had been stuck in. So I tried returning to the hangar, and just as the pad was beginning to descend, the hyperjump sequence kicked in. So I rode along, mostly outside the Carrier, through the jump. Didn't see the black fog though, the view suddenly updated to the new system.