ReplaceMagicHelp

Links in SharePoint Wiki pages - in case that you have relative links, for example /SomeFolder/Sample/book.xlsx, in pages which are in site with URL like https://replacamagic.sharepoint.com, which you want to convert to absolute links like https://replacemagic.sharepoint.com/Shared Documents/Sample/book.xlsx ReplaceMagic will trigger this change but after saving content to SharePoint, SharePoint will remove starting URL as it is the same like starting URL of document containing this link so when you rescan document again you will see that your link is changed from /SomeFolder/Sample/book.xlsx to /Shared Documents/Sample/book.xlsx. Unfortunately, this is not controlled by ReplaceMagic. 

Of course, when you properly set links new relative link will also work.