What are you having trouble with, exactly? Although we can help you out on this forum with any technical difficulties, we can't really build the app for you. In other words, maybe it's easier if you break your problem up into smaller problems and ask for more direct feedback.
That being said, the recommended way of getting files "into" mendix is by uploading them via the browser. If you can't do that for whatever reason you're stuck with a java action.
Like Achiel mentioned, you could retrieve xml files with java. That would be step 1.
Then you need a xml-to-domain mapping to map your xml into mendix objects. Set "validate against schema" on true. This would be step 2.
After the xml is mapped to objects you could update the objects with microflows. That would be step 3.
se a domain to xml-mapping to create xml files with the updated mendix objects. You could use a same sort of java-action to send the new created xml files to a folder.