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Transactional Replication - Backfil Data after failed publications

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We have setup Transactional Replication that was originally initialized from a backup. Our subscriber recently had some hardware failures causing the publications to fail. We now have the server back up however the transactions for a few days have been missed, and data is now out of sync.

How do I go about resyncing that missing data? We have too many table to manually resync the data, and I cannot restore the database directly from a backup due to some permission issues and differences from the publisher. I've attempted to generate a new snapshot however I get a message "[0%] A snapshot was not generated because no subscriptions need initialization."  My current understanding that is that I should be able to take a snapshot from the publisher and apply it to the subscriber, thus syncing all the data.

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