Like some have hinted at already - Google doesn't care for your link building building campaign, you done them manually yourself and they weren't natural - maybe Google is on to you manipulating their search engine and breaking their golden rule... why waste your time on such efforts? Focus on your own site and content!?
you checked the blacklist checker tool? and it says error free? so maybe the site is ranking high but you don't see it? sorry for the sting but you really can't trust any tool and it doesnt matter what any tool says, the fact is your backlinks disappeared and thats pretty much it. what you can do it build new backlinks in more authoritive places and invest in good relative content, basically you just need to go about with your seo and take into consideration this isnt really a rare sight.