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Log shipping involves applying a database's transaction log backups to one or more other databases. The databases (schema and data) are all identical when all transaction log backups have been applied. So no, you cannot perform log shipping when the source and destination databases are not identical.
In the scenario you described, you might want to consider replication, where only data in selected tables are synchronised. You could also consider other Red Gate tools, like SQL Compare, or SQL Data Compare, to synchronise schema and data.
To set up log shipping, whether using standard SQL Server tools, or SQL Backup, the destination database must first be restored using a backup of the source database. From then on, any transaction log backups you take of the source database must be applied to the secondary database. See here for some details.
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I would like to setup Log shipping to transfer data from Server A(having
database A) to Server B(having database
The databases A and B already exist. the structure of both these databases is similar although the data is different.
Can I setup log shipping to transfer data from database A to database B in this scenario when the data is different?
What if the data structure as well as data is same on both source and destination, can we set up log shipping in that scenario?
Please advise. If you could provide the steps that I need to follow, it would be great. Thanks!