Officially support flyway users updating the schema model directly. You can do this now, but even with identical t-sql in the schema + migration folders, flyway diff can produce false diffs.

This appears to be caused by how redgate scripts out the applied migrations (constraints in a particular order, using <> instead of !=) vs looking at the schema files directly.

I believe this could be resolved by running the schema files through the same scripting method so the end result t-sql syntax is identical.

See support request 340787 for more details.