DS-3097 applies separate database migrations to branches 5_x and 6_x. When upgrading from one to the other, the later version does not contain the migration script from the earlier, and this causes Flyway to complain about a migration with status Missing.
What I think is needed, is for the 5_x migration to be copied to 6_x. 6_x needs no migration of its own; that was only needed by developers while 6_x was being made, due to differences in the schema for that table. During an upgrade, the 5_x migration will fix any records that require it and then the general 6_x schema migration(s) will reorganize the table; during a fresh 6.0 install, the empty table will be migrated just as in the upgrade. To be clear: the V6.0_2016.08.23__DS-3097.sql script would be removed from the normal migration sequence, and the 5_x and 6_x branches would both have V5.6_2016.08.23__DS-3097.sql.
We might want to create a "developer toolbox" directory not seen by Flyway, to hold migrations that will be needed only during development. If someone needs such a migration, it can be copied to the place where Flyway will see it.