The .refactorlog should be in source control if you intend to move database objects across schemas.
See: MSDN: Move a Database Object to a Different Schema
Relevant section: Preserving Your Intent With The Refactoring Log
When you move a database object to a different schema, an entry is
added to the refactoring log for your database project. When you
deploy your changes, this log helps ensure that the corresponding
object in the target environment is renamed as you intended.
Otherwise, the existing object would be dropped, and an object would be added with the new name. The log is maintained in an XML file that
is namedProjectName.refactorlog. You check this file in to version control when you check in the other files that compose your database project. TheProjectName.refactorlogfile contains only information
about refactoring operations that require special handling during
deployment.