You could set up two different relationships that match the imported email address to one of the two email address fields. You could then use the relationship to set the related record's email field to "" to clear it.
In the future, you might consider setting up a related table of email addresses in place of two separate email address fields in the same record. This is more flexible in a number of ways. In this particular case, you could actually use Go To Related Records (Match found set) to pull up all matching records in such a table and delete them all in one go.
Perfect. Thank you!