If by chance you changed the names and didn't include a file extension I don't see how LR can see them. It ignores files that aren't images and any file without a file extension isn't seen as an image even if it really is.
The best thing you could do is use a file search program to locate all files on your drives that don't have a file extension. Search for Photo* (that's a Star, Shift # 8 key) and see what comes up. If you find them on your drives you'll need to rename them once again and include .JPG at the end of them.
If you are on a Mac don't bother with the built in search feature. Get "Find Any File" or "Easy Find". Two of the best Mac OS X search apps. If you are on a Windows PC there are many good file search programs.
If there is no LR edits to keep, or if you don't want to keep the existing edits, you could delete the files from LR and import them again.
Since the file names on disk and file names in LR don't match, you will need to manually match them up by hand individually, if you want to keep the existing LR edits.
The easiest approach to this -- without doing any script programming -- is to go into each directory, one at a time:
Select the correct folder in the "folders" pane. Right-click "show parent" as necessary to see the directory tree.
Sort the LR Library by creation date.
Using the details view in File Explorer, sort the files by creation date (add to the viewed columns if necessary).
Assuming no more than 1 image per second, the files should line up.
Renaming them in LR to match the name on the hard drive is not an option, it wont let me rename them in LR since the file is missing. And I cannot rename them on the Hard drive to match LR because when you batch rename files in Windows it always does it using the parenthesis (1), (2), (3), etc. So I can never get it to match
This should work: