2) additional skill points bought with IOUs
3) Precompletion Pro skill
4) sidekick (are they usable from lvl 1 or 9?)
5) Virtual Reality Gaming Center progress (Passable Pilot skill in particular)
6) unlockable zones like Rooftops of Downtown?
Nothing, nothing, nothing, nothing, nothing, nothing. In that order.
Now, if you have spent those skill points, they'll be gone, but if they're just sitting there, they're fine. Transmogrification mostly just sets you at level 1. Now Retcon will have effects on all sorts of things.