if you left limewire open while dragging the files to the trash, you'll need to hit the 'refresh' button in the library of limewire. otherwise, limewire will act as though the file still exists, and will advertise that it does, failing with a File Not Found when someone attempts to upload it.

i suppose there's some logic that could be builtin that checks to ensure the file still exists before sending a query reply -- but that could become very expensive and possible not worth it.