It has nothing to do with your incomplete files (their preference list is in the incomplete folder called download.dat)
The preferences hold all the information about your LW settings (& more) stored in a file(s) within the preferences folder. When you delete it then the next time you open LW it will ask you to set some of the options again such as download location, shared folders, etc. That's why I'd suggest you make a note of the option settings before you delete it. Sometimes the LW preferences can become corrupted. It might have various side-fx. A simple deletion of them whilst LW is closed can breathe fresh life back into LW & eradicate some abnormal behaviours.