[5.01 Spolers] "The great escape"

[Cleretic]

Regardless, it's not a "plot hole" just because we weren't given a full travel log.

Yeah, there's a difference between 'plot hole' and 'thing we weren't told'. To be a plot hole it has to be something that actually breaks the story, that has no at-hand explanation.

The actual most likely answer: There's an NPC whose actual job is to pilot that skyslipper. His name is Yalfort. He probably did the ferrying. And we didn't see it, because it literally does not matter. (EDIT: Also they put down an aetheryte shard in the Empty for the duration of the Eden questline, so there's that, too.)