"Never" re-import photos that are already imported.
Follow instructions to "re-link" instead : Adobe Lightroom - Find moved or missing files and folders
To keep this from happening in the future, do all re-structuring (moving/renaming) in Lightroom, with one exception:
If you move entire photo trees to a new folder, or new drive, it may be best to do that outside Lightroom, then re-link as per instructions above..
You can search by name in Lightroom to find duplicates.
I have some photos that are greyed out and it says they have already been imported. I can't find them anywhere and I want to upload them into the correct folder. How can I find them or override the system someway and upload them again.
In Lightroom, click on All Photographs, expand all stacks, turn off all filters (Ctrl/Cmd-L once or twice), and the use the Filter Bar to search for one of these photos by file name.
I have already tried this and I have searched by several different filters including file name and it says there are no matches.
Show me a screen capture of your Filter Bar and in the same screen capture I want to see that you have clicked on "All Photographs"