You shouldn't need to do anything in your properties in FlashBuilder. Just delete the swc in the libs folder and add the new one.
FlashBuilder by default will look for swc files in the {project}/libs folder.
So, if you delete the folder in your "Flex Build Path" properties, go back to it, click on "Add SWC Folder", just type in libs (it will know to look in your project directory) and make sure you have the correct swc in the libs folder.
If you added a swc manually in the properties area via the Add SWC..., delete it in the properties.
This will get you back where you started.