While cleaning up a couple crafting leves I found myself at camp Iron Lake. I took care of business and decided I would port home to Gridania to further the story line. Used the 6 anima tele to go to Bentbranch and then hiked on to town to trigger the main quest.
I never 'tuned' to the Aetheryte at either Bentbranch or in Gridania. I was ******** around and ended up dead. When I did my return I was back in La Noscea at camp Iron Lake.
So... in case you ever wondered teleporting to a new Aetheryte does not automatically 'tune' you to it. If you wish to make it your home point be sure to click on it.
In hindsight it makes perfect sense that simply teleporting there would not make it my new HP, in FFXI you have to physically touch the crystal to change your HP to it.