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I can't say specifically what the problem is with the stored procedure because there is no information here about the error or anything, but in general, SQL Compare is not able to synchronize replicated databases because it does not detect that columns are participating in replication and script an sp_dropreplcomumn rather than an ALTER TABLE. Sometimes you can get it to work in certain circumstances.
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I am usually use red gate for comparing data and database schema. But I need to synchronise database (schema and the data). both the database are in replication. Every time I want to synchronise, it give me error with an stored procedure. but the stored procedure does not need to synchronise as it is already matching. Can you please help me in this case?