Hmmmm in theory it shouldn't alter the dash files. ...It's only meant to clean out the save files, user settings and cache, thats providing you're talking about the same disc as I am ...Please post a piccy of it. ...The best thing to do would be to open the disc up and have a look at the files on it just to be sure before running it.
...There you go then, if you only have a default.xbe, all it will do is clean the user data off the system, as per a 'normal' Refresh Disc. ...It shouldn't replace anything, as there's nothing on the disc to read and copy over to the HDD, if you catch my drift.