Merge replication Identity columns for already existing databases
Vikram,

If your remote sites are named unique, then you can utilize HOST_NAME() as a FILTER  while creating a Merge Publication, we are doing the same at our place. 

We have 2000 stores across USA, which we replicate (via Merge Replication) to our home office. All these stores have same schema across the board, so table ID is going to be duplicated across the board. To overcome the duplication issue, we utilized followings columns in our Replicated Articles:


Table ID
RowGUID (It will be unique per server at your remote location)
SourceStore (this is filter for HOST_NAME(), which will make record unique at the home office (i.e. Central Location)


Example: 

-Subscriber A Table X has ID column 25 with row data (a,b,c,d,RowGUID,Host_Name())
 -Subscriber B Table X has ID column 25 with row data (e,f,g,h,RowGUID,Host_Name())

Hope this helps with your issue.

Thank you,
HP