sql server (alternate): I have taken over a transactional replication setup that is being used
for fault tolerance (I know, I know...).

The scenario I am concerned with is where the publisher goes down due to
failure, so we need to point our application at the subscriber and start
updating the data there. We are not using the immediate updating option.

How do I go about re-syncing the publisher with the data that been added
to, or changed on the subscriber, when the publisher comes back online?

Thanks,

TGru

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you might want to use Merge Replication instead of Transactional
Replication.