Actually it DOES work.
However, only with the newer versions of the updater. So, make sure you are using the latest version. If you already are there may be a bug that needs to be ironed out in the code, in which case you should post a bug report in the EQ2Map forum, with relevant information like updater and windows versions.
btw: you can also change the attributes of files through the windows explorer (in XP and 2000 atleast, not sure about vista). Open the folder and select the files you want to modify (ctrl-a for all) then right click one of the icons and select properties..