This is way overkill for what you want but I’ve use VS Code as well: https://code.visualstudio.com/ Available for free for Windows and Mac.
Out of the box it will only compare individual files:
Apparently there is a plugin available to compare complete folders but I have never used it.
I love VS Code but it really is a coding tool but maybe you can learn Python to help automate some of your ebook tasks 🙂
Winmerge is also free tool for that task that is often recommended but I’ve never used it.