On 2.1 sandbox.
Step to reproduce:
1.) Create contact John Doe with Home(Primary) email address email@example.com
2.) Create contact John Doe with Home(Primary) email address firstname.lastname@example.org
3.) Use an Individual matching rule that will trigger on matching First & Last name.
4.) On the 'Merge' screen, the conflicting email addresses are not displayed. If the records are merged, one of the email addresses is lost.
Preferred behavior: Both email addresses should be included in the merged record. Ideally, the user would be presented opportunity to select an alternate location, but as a minimum the second email address should be saved as an additional email address for the Primary location.
I believe this simple SQL would be sufficient for the minimally acceptable task:
UPDATE civicrm_email SET contact_id = $merged_id, is_primary = 0 WHERE contact_id = $duplicate_id;