I have a situation. My main site is hosted on SiteGround, which uses cPanel. I moved a second site to SiteGround as an add-on domain temporarily (to perform some tests). cPanel puts the content of the add-on site in a sub-folder of public_html by default.
The developer did not change the location of add-on site content to a sibling of public_html (a great practice). I realized this 3 days after my developer moved (a copy of) the second site to SiteGround, so I deleted the add-on domain and the sub-folder containing all the files right away. However Google had already indexed the second site as a sub-domain of my main site during that time.
So far I have not noticed any damage to SEO ranking of my main site and it's been 10 days. But when I Google site:mainsite.com, I still see pages from the second site indexed as both secondsite.mainsite.com and mainsite.com/secondsite.com
It's important to note that I received an email from Webmasters Tools about increased 404 errors 2 days after deleting the add-on domain and its sub-folder. I just checked Google WMT account and its still shows dozens of 404 errors related to pages of the second site.
I am thinking about using the URL Removal tool in Webmasters Tools to have the pages from the second site unindexed. But I am not sure if I'll be able to get secondsite.mainsite.com unindexed via this tool. I am not inclined to 301 redirect secondsite.mainsite.com to secondsite.com as both sites are completely unrelated.
I want to make sure that these 404 errors go away and my main-site does not suffer any damage in Google rankings due to duplicate content SEO penalty.
I would appreciate if anyone can help. Thanks!
