Yes after what I have experienced before, you can store it on different harddrives, you must just be sure to run wow from the right copy. and If you want to be real safe, then call your private server something else than World of Warcraft (Like renamiong it "Local Weather" or something)
If you get problem with this then use the IP swich metode on the realmlist.wtf and plz tell on this forum, cause then I'll not to myself that this does not work.