I delete an entity field using field_delete_instance and "Notice: Undefined index: id in conditional_fields_field_delete_instance() (line 1407" results.
The field I am deleting is not used as a conditional field trigger or target so there is no corresponding row in the conditional_field table. It seems that the conditional_fields module tries to tidyup when a field_delete_instance call is made but doesn't check to see if the field is used in a conditional field operation.