Just talked to RIM about this and they sent me the following (sorry about the "click here for 103302.sql file" as they didn't provide links):
Problem
You try to upgrade the BlackBerry Enterprise Server to software version 4.1 Service Pack 2 and the upgrade fails. The reason for the failure may vary (for example, the Transaction Log is full). When the original failure condition is corrected and you try to upgrade again, the BlackBerry Configuration Database upgrade fails. The DB_Install.log file displays the following:
[10000] (09/13 23:14:07.682):{0x1878} SQL Error Message from CBESDBInstaller::ExecuteSql.executeDirect: SQLSTATE: 42000 Native error: 3725 Message: The constraint 'PK_MDSConfig' is being referenced by table ' ', foreign key constraint 'FK_RelationSCMDS_MDSConfig'.
[10000] (09/13 23:14:07.682):{0x1878} SQL Error Message from CBESDBInstaller::ExecuteSql.executeDirect: SQLSTATE: 42000 Native error: 3727 Message: Could not drop constraint. See previous errors.
Workaround
To successfully upgrade the BlackBerry Enterprise Server, complete the following steps:
If you are running Microsoft SQL Server 2000 with SQL Query Analyzer
Click here to obtain the 103302.sql file.
On the SQL Server, open SQL Query Analyzer.
Select the BlackBerry Configuration Database name (for example, BESMgmt) from the drop-down list.
Open the 103302.sql file and run it.
If you are not running Microsoft SQL Server 2000 or do not have SQL Query Analyzer
Click here to obtain the 103302.sql file and save it on the BlackBerry Enterprise Server (for example, save the file to C:\Program Files\Research In Motion).
On the computer running SQL Server 2000 or Microsoft Data Engine (MSDE), open a command prompt.
Type the following command:
osql -d <database_name> -i <path>\103302.sql -E
where <database_name> is the name of the BlackBerry Configuration Database (for example, BESMgmt) and <path> is the path to the SQL file (for example, C:\Program Files\Research In Motion\103302.sql).
Note: The -E flag uses the permissions for the account currently logged in to Microsoft Windows® to access the SQL Server or MSDE database. If you do not have sufficient Windows permissions, or need to use a SQL Server account to log in, replace -E with the following:
-U <account_name> -P <password>
where <account_name> is the SQL login name, and <password> is the password of that account.
Press ENTER.
When the script has finished running, close the command prompt.