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cmatchettFlag for United Kingdom of Great Britain and Northern Ireland

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SQL SERVER System Databases

I have uncovered an environment that has two sites, with an SQL Server at each site.
Site1 - Server: Sever1
Site2 - Server: Server2

Each server is running SQL Server 2008 R2.  Site 2 acts as type of a DR site and CA XOsoft is replicating the data directory of Server1 to the data directory of server2. The SQL Services are stopped on Server2.

What initially came to my mind are the system databases for each server, as the copy has overwritten the system databases of Server2.  I also thought that the databases should replicated using SQL internal replication mechanisms.  There is a transactional replication job within Server1 but obviously isn’t working.

This certainly cannot work?  I understood that SQL Server system databases are unique to each installation?

What are your thoughts?
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system database cannot be replicated....