Providing LW was properly closed before you replaced the gnutella.net file that should be fine. Did you check in Task Manager to make sure there was no LW process running?
Did you also try deleting the whole preferences folder (named LimeWire)?
Go back to the gnutella.net file, hover your mouse over it...what size is the file?

Did you also try updating your Java version? Make sure to remove all other Java versions installed, before installing the new one.

Could you please give us your system details? In this thread If LW Will Not Connect
there's a link to click on, which explains the details that we need.