According to a Cocos2D guide a copy of HD tmx files for every SD one you have, adding the indicator "-hd" at the end of the filename. The tilewidth, tileheight, spacing and margin properties all need to be twice as large in the HD verions. Finally, the HD tile atlas needs to have -hd at the end of the filename, and it needs to appear written this way in the HD tmx file.
http://www.cocos2d-iphone.org/wiki/doku.php/prog_guide:how_to_develop_retinadisplay_games_in_cocos2d
I have lots of SD tmx maps that I often make changes to. Is there a process people usually use to make these HD versions automatically? The only thing I can think of is running a script in Xcode's build process, but it sounds like a nightmare.