Yes it will.
It actually is able to detect that difference, and then not asking you if you want to update would be rather stupid.
At least I'm certain it asked me a couple of times in the past...
What Cygma was going on about is the unlikely case of someone switching back and forth between two servers who are running different versions of a map, that person would then be prompted the "Your version of the map differs from the one on the server"-Warning everytime he was switching.
But again that really only becomes a problem if the maps on the server are not automatically updated via mwllmaps.com, in which case every server should be running the most recent version anyways. If instead it has to be done manually, well that's a serveradmins responsibility anyways, and since pretty much every serveradmin for mwll is more or less active on these boards that shouldn't be too much of a burden.
Also, as mentioned before state the version of your map in the headertext which is displayed right above the loadingscreen, and no one will miss it.
...unless you have tits in our loadingscreen, in which case I doubt the quality of your map, if you have to distract players like that...

// oh wait, CGB [Ancient Demise] included the map name in the file path as well. This is not necessary and was specifically also not recommended by the devs, yes. Including the version number in the map name, i.e. in the name defined within the xml file, is supposed to be sufficient, so that the auto downloader will always download the correct version.
Wait, now I'm confused now! happy now?!?
see what all that renaming leads to?
