Actually, deleting the " .limewire " preference folder should not cause you to lose your Incomplete files, since the .bat & .dat file containing the information of the already started downloads is in the Incomplete folder, not the " .limewire " folder.
What you will lose is the LW configuration information (i.e. language, listening port, folders shared, etc). This configuration you will be ask to re-do after starting LW again.
Anyways, glad to hear that it worked out.
