FeedDemon FAQ: Why did upgrading to FeedDemon 3.0 delete some of my unread items?

They weren't deleted - more likely, there were marked read as part of the conversion to Google Reader. When you add a feed to Google Reader, it automatically marks all but the ten most recent items as read.

And since FeedDemon defaults to displaying only unread or starred items, it probably looked like these items were deleted - but they're still there. You can view them again by changing the newspaper filter (shown below), which appears above FeedDemon's feed bar.