Thanks. But, yes, I have tried. There is something called CCleaner which can find all duplicates across many folders. But, unfortunately it displays the duplicates on a case by case basis. So, unlike WinMerge where you have the tree view and could select ranges of duplicates and deal with them in one go, you’d have to do it duplicate by duplicate. It also doesn’t have the text comparing features that were helpful in this process.
In the end, I understand that this isn’t really an Obsidian specific issue. However I felt that this was important to have opened up this topic for comment before I create a feature request. Because the ideal solution would be one that manages this problem and also deals with correctly auto updating links during this process.
Thanks again for your help!