Previously, when Magento was single connector then we used to check duplicate using etail customer ID field but now after migrating to the multi-account connector, we have started using "Celigo Magento 2 Customer Id Map" to keep track of customers and duplication. We have seen their previous lookup criteria that has updated that's why we haven't updated via migration.
If you want to use "Celigo Magento 2 Customer Id Map" record type to keep track then update lookup criteria for this:
Primary: [["custrecord_celigo_mag2_mcim_nsid.custrecord_celigo_mag2_mcim_mag_cust_id", "is", "{{id}}"], "AND", ["custrecord_celigo_mag2_mcim_nsid.custrecord_celigo_mag2_mcim_instanceid", "is", "#####"]]
Secondary: [["email","is","{{email}}"],"AND",["custentity_celigo_etail_isguest_customer","is","F"],"AND",["custentity_celigo_mag2_instance","is","@NONE@"]]