Once you have access to the Secondary Email field and are merging a record,
- Select the record with the email address you want as the primary email to be the Master Record and click Next Step
- Click the Merge icon under the Duplicate Record heading
- Highlight and Copy the email you want to keep from the Duplicate Record and Paste it into the Secondary Email field in the Master Record
- Check the box beside other information you want to keep from the Duplicate Record, if any
- Click Save
Related article: Can we send email to the secondary email?