How Do We Explain Ryne?

[Sigiria]

So, firstly, if you haven't played Shadowbringers to the end, don't read any further. Please. No spoilers.

Now that that's out of the way.

So Ryne is from the first. She's also part of the Trust. We know that the Trust is carrying over to Endwalker (hence the recommendation we level up our Trust NPC's before then).

We also know that we are getting Estinien as a Trust NPC in Endwalker.

So my question is, will Estinien be replacing Ryne in the Trust?

If not, how will they explain her presence in the Source for dungeons?

This question has been bugging me and the only thing that makes sense is that she won't be able to do any dungeons except Shadowbringers... unless Graha finds a way to bring her to the Source... but why would he? How would they bring Ryne to the Source?

They most likely won't.
During the first go at a dungeon you've got a specific selection of characters that are cannonically present at the time, after that you can return in the dungeon with characters that shouldn't have been around at the time of the events. It'll be just the same.