I have read everything from 'the set bonus is tied to the Armoring now' to 'the set bonus is on the shell until you remove the Armoring, and once removed the bonus will transfer to the Armoring'.
The latter is what scared me, cuz if I needed to I would put in 61 or 63 armorings into my old rakata shells and just rip those out for the set bonus after 2.0. Really hope my gear doesn't change tho!!
It's my understanding that everything will remain the same as it is now except in the case of existing Tio/Columi/Rakata gear. Currently those gear sets get their set bonus features from the shell and not the armoring. If you move that armoring to an orange currently you don't get the set bonus.
The only change is that post 2.0 removing the armoring from a tionese/columi/rakata shell will transfer that set bonus to the armoring so that the lower level armoring act the same way as the Campaign & Dreadguard do now. All future armor pieces will carry the set bonus in the armorings instead of shells like Campaign and Dreadguard do now.
You should not have to worry about your campaign armorings in your orange gear. The only change will be that ppl currently wearing Tionese/Columi/Rakata gear will be able to move those mods to custom gear and retain their set bonuses, which is something they can't do currently.