Hopefully it’s not too late to help save you (and others) some time and worry.

I just updated my install using ‘git pull && npm install’ and it actually aborts if it detects the update will overwrite files you’ve changed (pretty awesome feature imo).

Also, you don’t need to copy your main folder or even move any files elsewhere - all you need to do is rename the files it says would be overwritten with the update, and you can leave them in the same folder.
For instance, it said my main.css had changes and would be overwritten. I just renamed it to main2.css and left it where it was (and did similarly to a few other files).

After updating to the latest MM, I just went to the css folder, opened up that file (sudo nano main2.css), then saved it overwriting the newly updated version (saved to main.css).
That’s all I did for the few files I had customized and upon restart, all of my changes were present. Good luck!