When i go through the door (behind xydusa) to the fountain to cure, when i come back to
the room where xydusa was to begin with, shes gone.

Do i see here again later or is this a bug?

She could be somewhere in the maze adjacent to where you first encounter her. I believe there's a switch in the room with the healing fountain, did you flip that by chance?

She somehow got into the hall that the switch at the fountatin opens up.

There are two versions of Xydusa. One is a fake, which wanders down a hallway and is supposed to disappear to give a sneak peek of what's to come (you can trick it into staying, but there's no purpose - screenshot of the twins below - the right one is the "fake"). Another is the "real" Xydusa, who you may have not encountered yet. If it disappeared, and you couldn't damage it, it was likely the first one.

I somehow managed to get Xydusa to follow me to the elevators. Dodged around her a few times. Then when I got to the Headmaster's room, I activated the elevator to get out, then came face to face with her. I managed to huddle aginst the walls, before the elevator went back down...

Next time I knew, while I'm preparing to make a run for it, Xydusa gets herself stuck in the elevator going down, then dies after 30 rounds of 3-7 hp crush damage. FROM the elevator.

That was the easiest 10000+ exp I've ever had..

{spoiler}

The 'correct' way to handle this is giving kerielle(windmill near valeia) algamesh's amulet(first locked door in the crypt), she gives you an one-use potion (grenade, really) that you use on xydussa to put her to sleep when you first encounter her (face to face, not the through-the-bars show). Then you go to elyssia, drink the nectar she offers you - this gives the drinking character the "snakeskin" trait (she does not offer drink if xydusa is dead), then kill elyssia for the mask, go back, and finally kill xydusa.

As long as I've had this game, I've never known about this. I've always killed Xydusa at the earliest opportunity.

Me too, and i also think that along with the High Priestess, she is the only difficult boss fight :D