if you have checked out the document to the file system and removed the password protection you can put the file back to a document tray and then check it in again. When checking out to file system it is important to not change the file name as this is the only connection between the file and the original version in the file cabinet.
You could also use the edit functionality inside the file cabinet or document tray (depends on your rights) to open the document directly from there and save it. After closing the application it will be automatically uploaded to the original location. Depending on your file cabinet settings the new file replaces the original file or is added as a new version.