While you can upload and save any FDX files to Final Draft Vault, you can only open and edit those files in Final Draft Writer if they were most recently saved in Final Draft 13.
If you attempt to open a file that was saved in an older version of Final Draft, you will receive the following error message:
As the error message states, the solution is to open that file in your desktop version of Final Draft 13. Then save it (File > Save). Upload this version of the file to Final Draft Vault. You can then open it in Final Draft Writer and will no longer receive that error message.