How are linked records affected when records are merged?
When records are merged data may be overwritten and addresses may also be merged. Therefore, changes are applied to the primary record (record that gets saved).
When synchronization is run these changes will update from Education Edge to the linked Raiser’s Edge record. If the merge was done in Raiser’s Edge the changes will update from the merged Raiser’s Edge to the linked Education Edge record. The changes will affect only synchronized fields.