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I would do it basically how you mention. Assuming your database is the one with the most recent and correct data then I would first clear out the lists of contacts in your Constant Contact account. Then submit your new/updated list of contacts to the correct list within Constant Contact. If you want to use bulk methods here is how I would order them.
1. http://developer.constantcontact.com/docs/bulk_activities_api/bulk-activities-clear-contactlists.html?method=POST (this can be used to clear both lists with one API call)
2. http://developer.constantcontact.com/docs/bulk_activities_api/bulk-activities-addcontact-multipart.html?method=POST (this is used to POST contacts using a csv file to the list)
3. http://developer.constantcontact.com/docs/bulk_activities_api/bulk-activities-addcontact-multipart.html?method=POST (same as step 2, just do this for which ever list you did not pick in that step)
Using those import bulk methods sets the parameter to ACTION_BY_OWNER which means you will not be able to add contacts that have unsubscribed.
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