When you move to version 2 will the projects in the builder be deleted.. Or will the structures still remain, they will just need rebuilding with the generator?

You will be able to keep them, and to choose in which version to generate.

Some variables will be renamed in the wizards.
Because Joomla impose the var names when you use them for example :

author => created_by

And some others.
So if you was using them, no problem but the physical names in DB may be changed.