If you did nothing more than delete the contents of the Incomplete file, it should not have affected the contents of the Shared file in any way. However, no matter how you arrived in this situation, if Limewire is not currently showing the contents of your Shared folder in Library, open Preferences and ensure that Shared is the designated folder for Saving. The entry should be /User/yourname/Shared (clicking on the default button should bring it back to life). If, by mistake, you have actually changed the address of Shared, find out what the new address is by using Finder or Sherlock and put the new address into Preferences.