Lorenz - 9:39 am on Feb 15, 2013 (gmt 0)
In 2005, Site3 went online. Then in 2006, Site1 followed. Both targeting a different angle in the same niche, like "blue widget tips" and "blue widgets online".
Both sites were ranking well for its keywords, not competing with each other, received plenty of organic "good" backlinks. Unfortunately I made the mistake over the years to submit articles to directories like isnare and ezzinearticles. Like so many, I then received a manual penalty in beginning of 2011.
Both sites penalized, and ranking nowhere.
I then started to remove "bad" links for Site3, but quickly realized that the backlink profile for Site1 was so "messed up" in terms of volume of bad links, that I created a replacement site: Site2. However, I never took Site1 offline, nor 301 forwarded it to avoid the transfer of the penalty to the "fresh site2". I also started to ask webmasters to replace the link to Site1 with the URL of Site2. About 75% of the links were changed till now.
Until end Nov. 2012 I managed to get the manual penalties lifted. For both, Site3 and, for Site1 unexpectedly as well.
However Site2 (the replacement for Site1) never really took off, even though it has the better link profile now that it's predecessor (Site1), after changing the links. It's ranking on Page 10 for its main keyword. The link profile is well balanced out, anchor text wise. The site however is only 3.5 months old though. Maybe Google has seen that suddenly links from one site got replaced in favor for another but couldn't spot a 301 to undermine that redirect?
Does this make sense?