Yes, Fetish Core will be updated for the expansion. I'm planning to take a copy of the beta UI this weekend to compare with the existing UI for needed changes; trying to update it too much earlier results in a lot of excess work as they change things over the course of Beta.
Ideally I will have v12.3 (the CoE update) ready by launch, barring any unexpected major changes. There's always the chance they will change things between Beta and launch as well, but Fetish Core is designed so that the major HUD windows (like the character window) draw from the default automatically and thus don't need to be reworked each time.
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