Are u sure it's permanent? It can take LW several mins to account for all the files in the shared folders after LW opens. It's best to wait until the no. of files LW says it's sharing (bottom-left, front window) has been fully counted.

But then, if you trashed LW's dwnld prefs, your partially dwnlded files could be in a spot of bother. For shared folders, you might need to reAdd them. I don't suppose you made a backup of downloads.dat (found in the incomplete folder) before you reinstalled LW? When u reinstalled the os did u also reformat the HDD & change anything?