Currently, original faf client cant be used for map uploading.
Download Downlord's faf client from here to upload your custom maps to vault.
Close original client and install Downlord's client.
Upload map to vault by using Downlord's client.
To upload new version of map:
Do not rename map if you want to make new version, (for example supremecommandermap V2).
Instead, open your map's scenario.lua file and increase the variable map_version.
You may need to add that line if you have clean editor-generated scenario file. See attached picture.
You dont need to rename your map folder and map files anymore. All you need to do is to edit that single line and upload new version to vault.
Note: If you have uploaded your map to vault with Downlord's client version which is v0.6.22-alpha or earlier, it can not be downloaded automatically. To get autodownload work again, get latest version of client, revise your map and reupload to vault.
See official announcement.