For any flyway command which performs a database comparison under the hood (diff, prepare), the following rules apply in relation to mapping the source schemas to the target schemas:

• For SQL Server databases, database comparison will compare objects in all schemas, irrespective of any schema configuration. Schemas can be suppressed from the comparison using filters.
• For other databases, only the schemas specified will be compared.
  • If no explicit schemas are set for the comparison source, then the source schemas will be assumed to be the same as those specified for the target
  • If no explicit schemas are set for the comparison target, then the target schemas will be assumed to be the same as those specified for the source
  • If explicit schema model schemas are set for source and target, then source schemas will be automatically mapped to target schemas in the same order as they are specified