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Punk still has to vacate. The World Title goes through mostly the same lineage.
Trios titles don't get vacated, Elite are on TV through the Full Gear cycle, I assume this just equals a longer reign for the Elite and no best of 7 and instead more of a variety of opponents before they drop the belts to House of Black and move on to BCC.
Punk might show up on TV to cut promos and do commentary while he's injured, he might just go away entirely.
The backstage issues probably just keep festering under the surface and blow up at a different time, unless somebody decides to get control of them.