Lightroom is not a file browser. It does not show you the photos in a particular folder, unless they have been imported into that folder using "ADD", or somehow copied/moved into that folder via Lightroom methods. So there is nothing particularly wrong with Lightroom not seeing the photos you have placed into that folder using your operating system.
Your problem is that the photos exist somewhere in the catalog already (possibly because you accidentally used "Copy" or "Move" on import). Importing or synchronizing will not solve the problem. The solution is to find the photos in your Library Module and then (if desired) use Lightroom to move them to the proper folder.
To do this search you must do all of the following 4 steps (not one or two or three of these steps, but all 4 steps)
- Go to the Catalog Panel and click on All Photographs
- Turn off all Filters using Ctrl-L once or twice
- Expand All Stacks
- Search for the photos by file name