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Transactional replicated articles Identity Specification changes when Publication was scripted

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I recently scripted out a Publication on my SQL 2008 R2 (Standard) Server because I was in the process of restoring the publishing database and needed to tear down/ rebuild replication. After restoring, running my script to recreate replication I noticed that the the tables in the subscriber went from having their Identity Specification set to Yes to No. 

I had manually tore down and rebuilt this same publication in the past, without scripting, and not seen this behavior so I used the UI (SSMS) and did that again. This time the identity specification was back to Yes on the columns where it should be. 

Why would scripting out an existing publication cause this to happen? What setting or behavior am I missing?

Thank you



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