If you are upgrading from version 12.x or earlier, we implemented a change to the way the phone/email types are updated.
For general information about the phone/email types change (implemented in version 13.x), see this Knowledge Base article
During the updating of the phone/fax/email types to the new system, the current order in the Phone Types currently used (listed under Program Setup > Custom List Setup > Phone/Fax/Email Types, from version 11.12.26) will determine which one is the Primary.
For example, if there are multiple email fields, the one listed first in the Email Type list will become primary. If a contact only has the second email type, that one will become the primary for that contact, etc.
If you already updated to version 13.x or later, this change will not affect you. It only applies during the initial update.