Flyway 3.0 (due out tomorrow) will let you configure the separator. You can then change the default __ to . to suit your naming convention.
There is however no direct upgrade path from 1.X to 3.0 as the metadata table format changed in 2.X.
Users are advised to do an upgrade to 2.3 first, which will migrate the metadata table automatically, before migrating to 3.0.
In your case that won't work automatically due to the non-standard naming. You will have to convert your metadata table manually as a one-off as part of the upgrade. To help you get started with this, you can take the regular upgrade scripts packaged with Flyway 2.3 as a base.