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published database restoration failed once you setup transactional Replication using system Store procedures. Few work around to this problem is restore with KEEP_replication option and than drop the publication and subscription.

Is there anything we can do while setting up the Transactional replication using System SP that can avoid this issue ?

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Use below query to avoid replication related SP in Transactional Replication.

SELECT name 'ROUTINE_NAME','T' 'ROUTINE_TYPE' FROM sys.tables WHERE OBJECTPROPERTY(OBJECT_ID,'TableHasPrimaryKey') = 1 AND name not like 'MSpeer%'

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