Contacts which are merged are combined into one new contact. When a new contact is saved, the "old" contacts are removed from their original source. This behavior is due to Apple policy.
Therefore contacts that were merged are located in another source where they were saved.
Suggestions to view the new merged contacts:
1. Check the device settings to see which source is chosen to save new contacts.
- Settings>Mail, Contacts, Calendars,>Contacts>Default Account
- If the contact is set to save in Google or another account other than the device, please check that account to see the contacts.
2. Set which contacts will appear in the device contact list.
- Go into the native contact list>Groups>Show All Contacts.
More information about the Merge feature:
http://syncme.helpshift.com/a/sync-me-contact-sync/?s=premium&f=about-contact-merge