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I have a database under SqlServer2005 Enterprise 64bit sp3, that is in phase 3 of 3 of recovery after a reboot without normal shutdown.

It looks like with fast Recovery, the database became available when recovery moved into phase 3. However, it seems (based on message in SqlAgent log), that SqlAgent is "started" but not available to run jobs until recovery completes. I have other databases on the same server that are transactional publications.

It seems to me that if I let users update the published databases, transactions will start to build up in the log, but won't be moved to the distribution database or onto the subscribers because SqlAgent isn't running jobs. Should I be overly concerned about performing updates before

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You are correct, SQL Agent will not start until all databases have finished recovery. Because of this the replication jobs will not start running.

The transactions will pile up in the transaction log, until the log reader job is started. The only thing to be worried about is that the subscriber is currently out of sync, and will be until the recovery completes and the log agent starts grabbing transactions for the distribution agent to send out.

Also depending on how long recovery takes, you could run out of log space if you have enough transactions as the log can not be cleared until the log records have been pulled into the distribution database.

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