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Snapshot Rollback Issue


We have Transactional Replication set up between two SQL Servers on the same network.
This worked fine until one of the Servers was disconnected for some time.
Result is that we have to remove Replication to that Server and set it up again.
All appears to be ok during the set up,
However, when the snapshot is applied on the subscriber, it completes and we get the message
that the Snapshot has been delivered.
It looks ok for a few minutes, but the snapshot then starts over again, and undoes all the previous
replicated data.
Any ideas how to solve this or stop it from looping?
We can see that the snapshot tries to apply some scripts in bulk, that fails, so it tries them individually.
Could be one of these scripts is failing, hence the rollback?