Peter, all top level books except the last three are in one project (main child). Each of the last three books is its own project.
Two questions but one answer.
If you do not have topic to topic links between the main child and the other projects, then you can do what you want quite easily.
If you do have topic to topic links between the main child and the other projects, then those links will break when you generate the help. Links between topics in the main child will still be OK and links between the other child projects will be OK.
It sounds like you are using the method of merging described on my site where the parent is virtually a shell containing a redirect and holders in the TOC for the child projects. What you now need to do is regard your main child as the parent and put the holders in the TOC within whatever level of book you want. The holders do not have to be at the top level.
This is covered in an old topic on my site.
It does include a method of having links between any of the projects but it is tricky and I no longer recommend it. It was a solution before the better method was found.
Backup your whole setup before you start playing.
See www.grainge.org for RoboHelp and Authoring tips