I have created a Custom Group for Events. This Group has one custom field Organizor which is a autocomplete with contacts. But on merging the contact the Organizor custom field is not updated accordingly.
This is something not handle in CiviCRM at the moment when two contacts are merged. I am not sure if any one has submitted fix for this issue. You can either fix this by adding code to update contact_id for all contact reference custom field in core or through hook_civicrm_merge hook via extension.