I was doing the Greenshade quest "Striking at the Heart", and had gotten my second crystal, but not put it in the pedestal. This removed the phasing boon, as expected.
I then ported out (oops), emptied my bags, and came back to return. It turns out I didn't regain phasing after I reentered the bridge at the start of the instance, with the wildly over-powered enemies all over the place. Who could see my non-phased self, and massacre me in literally one ... barrage of shots, basically.
I was able to get back into the inner chamber and resume by running, using a soul stone to rez in the same place, and repeating that, then jumping through the door.
That was neither fun, nor easy, though, and it feels like Indaenir needs to put me back into phasing when he pops up next to me on the bridge, or at least, to be able to get it via talking with him.