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If I put a replicated database in single user mode will the Log Agent count as the single user?

ALTER DATABASE [DatabaseName] SET SINGLE_USER WITH ROLLBACK IMMEDIATE

I'm trying to block users from connecting to my database while it is being updated in the morning. So I was thinking of putting it in Single User mode, run update then put it back in multi user mode. But the database is also a publication database.

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Yes you can do that. Before hand make the log reader job disabled. This will make sure the jobs are not looking for the database.

For more clarity look at the below link :

MSDN : Replication and Single user Mode

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