Yes - it works fine on the QA site.
I'll describe how I tested here:
Step one - Create a new assignment with "File submissions" and "Feedback files" enabled.
Step two - Login as a student and upload a file submission to the assignment (I uploaded a Libre Office document).
Step three - Login as a teacher and "Download all submissions" (From the drop down menu above the grading table).
Step four - Extract all the files from the zip to a new empty folder (Should only be one)
Step five - Edit the document (I added lots of comments) and save it
Step six - Select all files in the folder and create a new zip file from them. (Do not just zip the folder)
Step seven - Choose "Upload multiple files in a zip" from the drop down menu above the grading table
Step eight - Upload the new zip file
Step nine - You should see that there is one new feedback file - click "Confirm" to save the files.
Step ten - Verify that one student received a new feedback file and it is the correct file.