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Can we do this by simply migrating the GL balances/transaction data from one database to another(i.e from R12 to 11i).If you mean you will extract the table data from one instance and then insert into the other then absolutely not.
That is not possible.
You will have to extract the data from source, validate it, insert into gl_interface on destination, run GL import, and then post the batches.
Alternatively, if all your business wants is updated totals (which is unlikely), you can simply extract period end balances, create journal entries for the differance (manually or programmatically depending on volume) and post them.