You might have to make changes to message flows and to the style sheet and XML files that they use when you migrate from Version 5.0 to Version 6.1.
If you do not plan to include the style sheets and XML files with the message flows that use them in the broker archive file that you deploy, and your XSLTransform nodes reference style sheets with partially-qualified paths (relative referencing), you might need to migrate both the message flows and the style sheets. If your XSLTransform nodes reference style sheets with fully-qualified paths (absolute referencing), migration is not necessary.
You can continue to deploy your style sheets and XML files manually into the broker file systems, but you must store relatively-referenced style sheets and XML files (and their dependants) in the broker work path/{XSL,XML}/external directories.
An embedded style sheet is handled in the same way as a file that is loaded from the root of the broker’s deployed storage, therefore move any descendant style sheets or XML files of embedded style sheets to the broker work path/{XSL,XML}/external tree. If you cannot move the files, you can reference them with a fully-qualified path (absolute reference).