Using Calibre only is a good idea, unless you want to buy books from the Sony store. If the OP is having problems with the Sony software and ADE already, adding another program might make things more complicated.
Originally Posted by Doc333
I ended up with everything on my reader duplicated, so decided to go back in and drag them out. Not possible as for some reason the software doesn't now recognise my reader as being registered to this computer.
You have to delete, one by one, the duplicate books on the reader. Problem solved. That has nothing to do with the software, it's because you clicked sync. Sounds like there are only nine books so this should not even take two minutes to do.
Your Reader is not registered to your computer. It's registered to your Sony account. You can have 5 or 6 devices authorized on one account; at one time I had four computers at once plus my Reader and they all worked fine.
You should probably just call or email Sony support and have them straighten it all out.