Unless you have somehow managed to locate your download folder inside your Limewire preferences or Limewire application folder, which some have managed to do and should NOT have. .... Then you will have no problem.
Just check the location of your downloads, and if you can't find them check by using Limewire Library>explore to see where your folde(s) is/are.
What ever you do do not delete them from the Limewire Library before removing Limewire. That way you will loose them
I hope this helps