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I usually only queue up for duty once a night (I am new)
It seems some skills on the bar downgrade automatically to lower level equivs, others do no, and not the same ones every time.
Am I supposed to keep a whole bunch of different level appropriate cross bar sets defined at all times and switch to whatever level dungeon I get called to? or is there a trick I am missing?
Skills will always sync to the max level of the duty that you're in. The only exception are Role Actions (Rampart, Swiftcast, Peloton, etc.) - once you learn them they will always be available, regardless of duty.
They should behave the same way every time. What you might be seeing are multiple versions of the same skill. For example, Holy has no upgrade so it should never change. Aero, however, has multiple different versions, so the skill will be different depending on the max level of the duty. You don't need to reassign them, the game will do it for you automatically
Each dungeon has a max level that can be used in it. If you are a higher level than that level, you are synced down to it, and you'll only have the skills available up to that level.
You shouldn't need to have multiple hotbars though. The vast majority of classes all build up over time, so they add on to their kits without removing anything, so your standard hotbar should work for them. The only real exception to this is Black Mage, as it has 2 spells that simply stop being used at a certain point. Blizzard 1 and Fire 2 are completely removed from your rotation after a certain point (really Blizzard 1 should just upgrade to blizzard 3 IMO) so there can be some wonkiness there if you don't wanna keep them on your crossbar (I know I don't).
Edit: Oh yeah, many abilities have automatic upgrades, so you don't need to worry about them. If you are concerned about needing to have a hotbar for like Stone 1, Stone 2, Stone 3, and stone 4, that's not necessary. They automatically change to the next or previous level whenever appropriate. Black Mage doesn't do that for most of it's numbered spells because each one does a different thing rather than just being an upgrade (thunder 3 and Thunder 4 are the exception to this, they upgrade thunder 1 and 2 respectively), but like I said I think Blizzard 1 should get the upgrade treatment to blizz 3. But that probably won't happen.