I hope your problem is Cisco CallManager publisher server has correct user data and one or more Cisco CallManager subscriber servers either do not have user data or the user data is out of date with the Publisher's database
The presence of invalid replication agreements causes the DC Directory database (files in C:\dcdsrvr\run\dcx500\database) to grow extremely large (over 100 MB) thus causing DC Directory to take a large amount of time to shutdown/startup.
In that case you have to reconfigure your DC directory on Cisco CallManager Publisher which has a database more than 100 Mb, which is decsribed in the following link.
http://www.cisco.com/warp/public/788/AVVID/fixing-dc-dir.html