Well this tool is not for beginners it states right there on the page and you needs to be addressed by a professionals if not you can do real irreversible harm to your website. Once you delete those backlinks you wont be able to get them back that is why Google is telling you that in your request there is a link that is important for your website it could be even one of your own ones!
Please create a topic here: http://letsforum.com/Forum-Website-Review
and include your site URL and the code you're submitting to Google.
It happened to me once with with robots.txt. I blocked some URLs on my site and Google told me that I was blocking important pages on my site so I fixed it.