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Most of it can be done while the server is up.  But some databases may be 
missed.  The command you are looking for is RUNDOMCMD.  It may be specific 
to newer versions of Domino for the iSeries.

The Run Domino Command (RUNDOMCMD) command runs an operating system 
CL command in the context of a particular Domino server.  It sets up
the environment which allows the command to be run whether the 
Domino server is active or not. The setup includes setting the PATH 
environment variable for the server, setting the directory for the 
job to the data directory of the server and running the resulting 
job under the QNOTES user profile. 
 
Restrictions: 
 
  1.  To use this command, you must have either of the following: 
 
       o  *ALLOBJ special authority. 
       o  *USE authority to the RUNDOMCMD object (object type *CMD) 
          in the QSYS library and *USE authority to the QNNINRUN 
          object (object type *PGM) in the Domino product library. 
 
  2.  If the CL command string is to be run in batch, BATCH(*YES) is
    specified, the RUNDOMCMD command setup does not set the 
    current working directory for the job to the server data 
    directory.  Instead of, the home directory of the QNOTES user
    profile is used.  A batch job does not inherit the current 
    working directory of the job which submits it. It uses the 
    home directory of the user profile it runs under. 

Rob Berendt

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