Robert_Charlton - 8:43 pm on Dec 21, 2012 (gmt 0)

But today when again looking at my main url site through the site: command I noticed that it is now showing the subdomain results also. In the past when I actioned site:www.(mysite) I only got the www.(mysite) results. But this morning when I action site:www.(mysite) I also get (subdomain).(mysite). The subdomain results without the www. A few hours later the site:www.(mysite) results were back to normal.... ...So... are they treating subdomains as if the content is part of the main url?

I'd hesitate to trust the site: operator to indicate much about how Google is ranking pages. The site: operator in particular has been notoriously undependable. That said, the interface often does reflect what's going on underneath.

Are you seeing anything to suggest that previously siloed subdomains are now affecting the rest of the site?

Conceivably, if there's much interlinking between Pandalized and non-Pandalized subdomains, that interlinking could hurt better performing subdomains, but that is only speculation.

In the long term, I myself would get rid of material that is low quality... not simply shunt it off to the side.