IF your download folder is outside the LW program folder, then no it will not affect them. The new version may choose a different location for downloads so beware of that; http://www.gnutellaforums.com/window...downloads.html

Some people thoughtlessly choose their LW program folder for their downloads. I am away sometimes LW program defaults to this location. O.o The best location is either your Account -> Documents folder, else even better is a second drive or partition so that LW incomplete files do not fragment your system drive which of course will slow it down.