Find that folder (the Shared folder), cut & paste it into a different location outside of the program directory. Perhaps paste it to the location I gave earlier.
ie: C:\Documents and Settings\"your account name"\Shared

You should also delete your LW Preferences folder whilst LW is closed; instructions here: Point #2 in Fixes for Limewire (sample at bottom of page.)

In that way, after you install the new version, it will ask you where you want to set your downld location. The default setting will be the one I gave. If you don't do this then it will continue to downld into the program folder which is not good.