A while ago, I posted Google Reader alternatives: did you make a choice yet? indicating this about Feedly:
PRO: GR imported posts contains all history (even from blog feeds that are now defunct)
Well, I was proven wrong by this Feedly posting about the migration to their own cloud: [IMPORTANT] Preparing to be upgraded to the new feedly cloud | Building Feedly.
The one part we did not migrate from google reader is your history (too much data) so you have to expect that you are starting from a blank history and your unread counts will be reset. This is a one time issue.
Is there any Google Reader replacement that imports full history?
–jeroen