If you have create a website that is located in a directory upper the master website and that you delete this upper directory, this result by deleting all the directories and subdirectories.
This is the only case that we see.
ie: /home/account/public_html/master
and you decide to create a slave site that is located in
/home/account/public_html
When you delete the slave site, this delete the directory
/home/account/public_html
and therefore all the subdirectories (including the /home/account/public_html/master)
To avoid such case, we have recommended an architecture in the tutorial video 0.b slide 21-24 where all the directories are specifics.
www.jms2win.com/tutorial#jms12x-0b