Complicated Question: Removing Spam Backlinks that were Not Requested

[web023]

I'm new and seeking help with the following scenario:

1. Main site:   is a domain.com    established authority type site

2.  Second site: is a  domain.org     (has robots.txt to no index) but someone obviously not site owner has done negative seo campaign against the .org domain and built spammy links to it. In fact, that's all that exist on this second domain because it is used for development purposes only right now.) No one would link to this one normally as it is just secondary domain used to protect trademark and for development use.)  When searching for it by domain name it does not appear on first page for search results.   Checking link profile the only links that show for domain.org are spam links.

Have contacted site/s where spam links were placed (no answer)

Main site  domain.com and domain.org have same whois and hosted on the same server as they are owned by same company

Main site domain.com still appears first for its name but has lost some rankings. I am working to fix some technical issues ie: duplicate urls with CMS etc, but would like to find out what to do about  the domain.org content that clearly has had someone target it with spammy non requested backlinks.)

domain.com has Google webmaster tools account, no messages about unnatural liking in those reports

1. I'm not sure I should add    domain.org to GWT to see if there is an unnatural link penalty applied or if this would further connect the two domains through association.

If I could get some feedback/suggestions on what my options are with regards to making sure that the  domain.org domain has a clean profile that would be most appreciated. Also because site owner has would like to begin using domain.org in the future for some unique content, but as it stands right now cannot because domain has been targed by poor backlinks.

Anyone else run into situation where the .org or .net versions were targeted by spammy backlinks even though the domains were not actively used?

What's the safest way to proceed?  a) Concerned about possible co-penalty between main site    domain.com and domain.org    b) how to remove problems issues with domain.org so that owner can use it in future.

Many thanks for your thoughts and help with this one. I appreciate any help or feedback.

[Debdulal]

Ok another tricky situation. First of all, I would like to ask you to create a Google Webmaster Account with a new Gmail id for this Domain.org [since you are worried about the association, though I can assure you there is no such thing as association with a penalize website will incur penalty for other websites ].

_So, you need to create a Google Webmaster Tools account to figure out whether the website has got penalized by Penguin update. If you have received any message in Google Webmaster Tools account regarding link warning, you need to get all the spammy links removed before applying for a reconsideration request. However, if this is an algorithmic penalty, you need to give a try to Disavow Link option. _

[SEO5Team]

Focus on the main domain and review the backlinks for that domain. If you identify any questionable links use the google disavow tool to submit information on those links.

Check the .org to ensure that the robots.txt no index is properly in place and none of the pages are getting indexed by Google.

[BlueprintMarketing]

I would write to Google explaining statically why you are doing it and how you think those links came about. I know that the system is set up so that if you're innocent like a competitor did that to you you would not be penalized.

The best of luck,

Tom