There had been instances where after upgrading from TFS 2005 /2008 to TFS 2010 there were Labels missing items or Merge relationships. This issue is addressed by a Hotfix and the information is available here: http://support.microsoft.com/kb/2193796
For more on this issue, please visit Brian Harry’s blog: http://blogs.msdn.com/b/bharry/archive/2010/06/25/tfs-2010-upgrade-issue.aspx
1) If you are yet to Upgrade to TFS 2010, This Hotfix has to be installed After TFS 2010 is installed on the server but before running the “Team Foundation Server Configuration Wizard”
2) If you have already upgraded to TFS 2010 and facing this issue, the scripts that will help you fix this issue is available on Brian Harry’s blog (Issue.zip). If you are facing issues running the scripts, please call Microsoft technical support at (800 936 5800).
TFS setup Team