Database error when reverting a feature with an relation field

When reverting a feature that contains a relation field, I get the following error. Please note that this is using an up-do-date repository, with update 7001 having run.

[jpathan@drupal-qa-jnl-web02 drupal-webroot]$ drush fr highwire -y
Do you really want to revert field? (y/n): y
WD php: DatabaseSchemaObjectExistsException: Cannot add index endpoints_entity_id to table field_data_endpoints: index       [error]
already exists. in DatabaseSchema_mysql->addIndex() (line 443 of
/opt/sites/jnl-ajpheart-testing/drupal-webroot/includes/database/mysql/schema.inc).
Cannot modify header information - headers already sent by (output started at                                              [warning]
/usr/share/pear/drush/includes/output.inc:38) bootstrap.inc:1440
DatabaseSchemaObjectExistsException: Cannot add index endpoints_entity_id to table field_data_endpoints: index already exists. in DatabaseSchema_mysql->addIndex() (line 443 of /opt/sites/jnl-ajpheart-testing/drupal-webroot/includes/database/mysql/schema.inc).
Drush command terminated abnormally due to an unrecoverable error.                                                           [error]

Under investigation, it appears that it is because the indexes in the database are in a different order than the indexes in the schema, resulting in field-api thinking the schema is out-of-date and tries to add the indexes, resulting in an error.