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It will only operate within BLADELOGIC and BLADELOGIC_INDEX. In that sense, no it won't.
That said there will be an overhead in activity and some additional space will be temporarily used, in that sense there could be a side effect.
One additional question to verify. Since I have a separate DB server, I assume I run the
migration_setup_OM.sql from there? Or should I run migration_setup_OM.sql from
my Appserver and have the Appserver connect to the DB server.
It doesn’t really matter where it runs from. it needs to run as a sysdba user, so if you can do that from sqlplus on the appserver fine. or from sqlplus on the db server, fine.