@Nyn - you are like a kiwidude plugin poster child...
With regards to lists with removing items, see the attached screenshot. It is introducing the concept of a list type. So you can make:
- a list that syncs only items not already on the device (default), or
- a list that always syncs all of its contents (for people who modify their books and want them forced back onto the device each time), or
- a list of books that you want removed from your device if they are present
For the first type of list, you will likely want "Clear this list after a sync" to be unchecked. For the second type you could go either way depending on what you want to do. For the third type you would probably want "Clear" to be checked.
Hopefully that will keep everyone happy. Just testing it at the moment and then will release it.