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.

Good luck.

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