This is answered in the FAQ: http://flywaydb.org/documentation/faq.html#How_do_you_repair_the_database_after_a_failed_migration?http://flywaydb.org/documentation/faq.html#repair
The upcoming Flyway 2.0 will include the repair command. This code is already checked into SCM.
Note: This only deals with Flyway's metadata table. You are still responsible for cleaning up any other effects of a failed migration.
Update: Flyway 2.0 has now been released. You can grab it at http://flywaydb.org