Last week after upgrading a TFS 2008 environment to TFS 2010, we discovered that our merge history was no longer correct. After some investigation I found this post by Brian Harry where he explains that their is a bug in the TFS upgrade process.
'”We have discovered a potentially serious issue that can affect upgrades from TFS 2005 or TFS 2008 to TFS 2010. The issue is triggered by a specific pattern of labels, renames, deletes and/or branches that existed before the upgrade. Once the upgrade is complete the contents of the affected labels could be incorrect. Also some internal merge tracking data could be incorrect, resulting in the need to reapply previous merges.”
There is already a hot fix available here: http://code.msdn.microsoft.com/KB2135068. Apply the fix after the initial installation, but before you start the Team Foundation Server configuration. Therefore uncheck the “Launch Team Foundation Server Configuration Tool” checkbox at the end of the installation.
Unfortunately you probably will only discover the issue when you start doing merges. So I suggest to run the scripts attached to Harry’s post to see if your environment is impacted. They describe it as a rare problem, but I was already able to reproduce the problem in 2 environments!