First thing - EXPORT the Inbox to an mbox file. Then Import it to a temporary folder (Create one under the inbox if you want. See if that helps and see if they are showing up in that folder. IF they are showing then go to the original inbox and use the information tab to get to the correct folder on your hard drive. When you get there you are going to delete the files in the original inbox (move them somewhere until you are done just in case you make an error.
Then in the Bat, drag the visible messages in the temp folder back to the inbox

Once you get that far you really should not keep that many messages in a folder as if it is gone you have lost the whole thing. You can archive them out or anything that works for you

Also run the maintenance center on a regular basis

Post back and let us know if that helps