Hi @sanjayap, currently if you use patient merge functionality of openmrs on possible DB of Bayalpata (which Akhil has suggested), it would error out because of the volume of data. This issue has been already identified + addressed but not available as part of 0.85 version of Bahmni, this would be available in the next release of Bahmni which we shall deploy at Bayalpata. Please see this pull request submitted to Open MRS to fix this issue.
As far as merging 2 duplicate patients whose ID you are already aware of, there is a open requirement in the possible health requirement list which is yet to be addressed to support this feature to search patient based on ID to trigger the merge process. Please see this mingle card for more details on the same. Please let me know if this answers your questions.