Is LinkFixer Advanced reporting more links in your files than you can find by visually examining the file?
We have seen this phenomenon before with Office files. We call these "phantom links".
There are certain steps your users can accidentally take, when they modify or replace links in their Office files, that result in the original link simply being submerged or hidden by the new link. If the new link is later removed, the older "phantom" link can still remain hidden in the file. When LinkFixer Advanced scans the file, it finds and reports both the old (phantom) link and the new link.
Unfortunately, from the perspective of LinkFixer Advanced, these "phantom" links and regular links look completely identical. So, we have not found any way to distinguish and eliminate these links from the LinkFixer Advanced reports. And, we have never found any instructions from Microsoft about how to remove them.
The good news is that LinkFixer Advanced is finding more links than you can see in the files, not less. If these phantom links are broken, they cannot be inoculated or cured by LinkFixer Advanced. If the phantom links are valid, it doesn't hurt anything if LinkFixer Advanced fixes these links in the course of your migration. Since they are invisible, most people consider that there is no down-side.