Are you on mac or windows?
my reply is based on mac layout, but windows isn't much different.
Do you mean that you have an duplicate LR catalog? When you open LR do you see all of your files? Is there a ? mark on the folders? It's pretty unlikely that you have a complete duplicate of your whole catalog. If one or the other is really complete and no ? on the folders (meaning that Lr knows where the files are), you can safely delete the other duplicate catalog (or if you are unsure just rename it so LR doesn't see it and be sure you have everything in the remaining catalog and then delete it).
Be sure you make all the changes using LR not your OS. If one or the other catalog has some ? folders, you can right click on the folder and select FindMissing Folder and identify it in finder and select it to remove the ? (meaning that LR knows where the files are).
Hope this helps...
tom
