Manual synchronization SQL Server enigma

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I've installed two SQL Server 2008 in two sites linked by internet connection and I've installed a merge replication between them, but one of the sites got a long disconnection time and the customer asked us for a manual synchronization (file-based) so they can make servers synchronized in this situation.

My simple question is :
What's the best tool to generate changes from both databases and apply the result to both databases ?

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If you can connect to both databases, you can use the tablediff utility.