[Junket]

Well that is what "all" means by definition. Probably the easiest way to get it the way you want is to change the way your books are organized on Calibre, then start over with the device i.e. side load your books again from the new library.

In your place I'd just create a new Calibre library and either move the Calibre books you want on the Kindle to that library - or (much better IMO) copy i.e. make duplicates of your existing books that you want on the device in the new library. That way your existing collections remain organized the same way and this new library are both duplicates and an accurate snapshot of what you want to display on your device.

For special offers it all depends on what the Amazon did when you called them. They may have just unregistered your device - ads won't show up until you register. Or (less likely) they may have removed the ads because of the change of ownership. Less likely because they usually charge $20 to effect that permanent removal of ads. And depending on how you did the jailbreak might impact this too.

You said that you always side load books anyway so you wouldn't gain much other than ads by registering. So not registering will keep ads at an arms length in either scenario.