The migration script encoding options within Flyway are defined by the Java character set.
In the instance that a scripts encoding is either mismatched or fails to be detected*, the product will fail silently forwards (a debug message will be displayed if debug is enabled) and will default to UTF-8 encoding. Depending on your script encoding, this may still work if the encoding you are using is sufficiently similar.
If you think this situation is occurring, please enable the debug switch to determine if the encoding detection is throwing an error.
*This assumes that the following parameter is being used.