Is it even possible to upload a new manuscript file to a current manuscript in the system should the author have done all revision work in their original file instead of in the system?
Currently, if an author submits a Docx, the file is converted to a flavour of HTML accessible in the Wax word processor. The idea is that any further edits will be done in Kotahi, using the Wax editor.
Should you wish to use a file submission, some work would be required to update the MansuciptsFile. In the meantime, you could use the Attachments form field type.