When XO scans your Custom Scenery folder it always checks all shortcuts, symbolic links and junctions. Sometimes scenery is moved to another location, but the link is not updated. For more explanation about shortcuts, symbolic links and junctions and what happens of the original folder is moved, see this article: X-Plane and links.
So how can you repair bad links? Simple: you can’t.
The only thing you can do is delete them and make new links.
If you make use of shortcuts, symbolic links or junctions a lot, you may find xToolbox useful. Not only can you easily create links with it, xToolbox also gives you overview (did I link everything?) and insight (where do these links point to?).
Furthermore, xToolbox will automatically detect badlinks and delete them for you. Much easier than finding them one by one with Windows Explorer.
You can find more about links and xToolbox here: XT and links