What you mean is when you re-open LW there's nothing left in the Library window? Try deleting your LW preferences folder whilst LW is closed; instructions:
Fixes for Limewire Also re-add your shared folders via Tools>Options>Sharing & press the Apply button after all additions & changes.
After a 2nd look at this post I realise you must be at least partly mistaken. If you have LW version 4.4 or later then you should have a folder within the Library window called Saved Files. This is default & there is no way of deleting this folder (well you wouldn't want to try.) This folder has your files that you've saved within it. Perhaps you can give us some more details & tell us which version of LW you have.