No version of Quark will save back more than one version - changing the extension (though they aren't different between 6 and 3) wont make a blind bit of difference.
Only thought if you don't have access to the intermediate versions is to get Markzware's utility - can't remember what it's called - that lets you save down through near enough all versions.
Remember the file will, almost certainly, 'fall to pieces' and will need thorough checking to make sure what you had in v6 is what you get in v3!
Good luck,
Greg