Once you have finished with the reconciliation, your CMD list will remember the links you have created, and it will have been updated already with the items you selected on the Fix Differences dialog. If there were names you flagged for updating in eAdventist, log in to eAdventist and make the changes there that you noted from your CMD data. Once this is done, your CMD and eAdventist files are reconciled as of this date. Subsequent reconciliations will be much simpler and much less time consuming once the initial reconciliation has taken place.
It's up to you how often you perform future reconciliations. You can download your current data form eAdventist as often as you wish, and you may perform the reconciliation as often as you wish. Do it as often as you begin to sense that your two lists are growing out of sync with each other.