"Clear inactive" only clears "awaiting Sourses"(whether partialy completed, or unstarted) & "completed" from the download window. The Awaiting sourses files whether partially or not downloaded remain in the library. Go to library >incomplete files to delete or resume them....this need not be done imediately. Be careful that you ONLY delete incomplete files, deleting shared files will permanently remove them from your computer. Do this when limewire is not busy as it can often hang the application for several minutes.

There is a possibility that searching for a particular subject may trigger an Awaiting Sourses file of that subject into restarting download, but generally it makes life easier to Clear innactive ... less clutter .... you can always try to resume later from the library, unless you delete the file from there. I'm not sure if leaving a lot of "awaiting sourses" in the download window matters from the technical point of view.