Here is what I think a good way of approaching the SEO issues in general is:
1. I cannot pin point that interlinking my sites got me penalized because there are other things that could led my sites to a penalty.
2. The key, I believe, is to make the sites SEO "safe", wait for a few weeks, months and start changing things slightly, always knowing what to change.
SEO safe means eliminating factors that can damage a site.
When you have too many factors that can damage the SEO how can you tell which one did it?
Take care ;)
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