Hi Kris,
Here are the steps to do it correctly without changing the flow.xml manually:
Whenever you want to change any package structure (e.g. folder and subfolder name etc.), start the Developer and create the new Package with the desired folder/subfolder name and drag and drop the elements (flow, java, document, schema…) from the existing package to the new package. Each time you do this this, webMethods will prompt you whether you want to update the refrence. Click on “Update Usage” and Developer will change them for you.
HTH,
Bhawesh.
#webMethods#Integration-Server-and-ESB#Flow-and-Java-services