I was trying to register DB2 enterprise geodatabases with ArcGIS Server through the Data Store but it would only let me register one database. Any time I would try to register another database it would say that the database was already registered with the server. No data was copied to the server during publishing even if the database wasn't listed in the Data Store.
The databases are cataloged using the Setup Assistant that comes with DB2. They only thing I can think of is that because one database is registered, it is referencing that catalog of databases so there is no need to register all databases individually with the server.
ArcSDE 10.0 is installed on the database server but we are moving away from ArcSDE to direct connect.
All databases have separate aliases.
DB2 enterprise geodatabases v10.0
Databases are stored on a Linux Server
ArcGIS Server v10.2.2
Windows Server 2008 R2
DB2 Client 9.7 is installed