When you delete the preferences folder, it resets all your options back to default...so the location of your saved folder would've changed back to the default

In LW go tools > options > saving. Now you can change the saved location to wherever you like!

Just check your days to keep incomplete files (tools > options > saving)...the default's 7 days. If you had the days to keep incompletes set for longer than that, you'll need to reset that. Otherwise you might get a nasty shock when your incompletes disappear.