I used the new Clone plugin to create a sub-domain site from our main site called southco.greensquares.me and it worked a treat!
I then deleted a number of blog posts from our main site to 'de-southco' it.
The southco.greensquares.me has now disappeared, replaced with the wordpress spam notice.
We have researched this and we have already done the move as instructed and as per Aaron on the https://premium.wpmudev.org/forums/topic/main-site-marked-as-spam forum.
The site is still not showing!
This multisite functionality is critical for our deployment