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Linked Query question

My Application updates/insert Data on two different SQL Server (Server 1 & Server 2) with same table name. so if Server-1 table A as 25 transaction than Table A on Server-2 should have same transaction(25).
I am missing some transaction on my Server-1 but are present on Server-2. so i want to query in such way that will look NOT IN server-1. as two server are involved, so i want to know how i can Linked Query NOT IN with two server.
Why you are using linked server to update from application, why not use replication in this case.
Check any issues while connecting to the LS-2 from application. Satya SKJ
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