You won't lose any settings. They are stored in your preferences folder which is stored here:
C:/Documents And Settings/your_username/.limewire
OR here C:\Documents and Settings\*yourusername*\Application Data\Limewire
(Application Data is a "hidden" folder.) The location depends upon which version of LW you started with.

Your downld preferences are stored inside your incomplete folder (download.dat & .bak)