I heard on another forum that if you install MM6 (and I am guessing any other MM games that use unofficial patches-like Grayface) to make sure to uncheck the "Keep game updated" box. Because if you don't, when GOG runs a new update it can wipe out the unofficial patches.

Is this this case? I don't think I unchecked that box. Has anyone run into this?

I would suggest you don't use galaxy. Use the downloader links. That way you can update a game only when you wish to do so. Saved my behind on Avernum when it's latest update broke compatibility with mods.

I honestly don't know how to do any of that. Downloader links? I use Galaxy because it's easier to do so, but it sounds like I may need to reinstall MM6, as well as Grayface's mod, eventually.

It is actually super simple and may be easier than Galaxy.
1) On the website bring up the list of your games.
2) Click on the downward facing chevron on the game you wish to download.
3) Click on view download.
4) Click on the downward facing chevron next to the word more.
5) Click on GOG downloader links.
6) That will bring up a list of hyperlinks, chose the one for installation. This will download a file on your computer. Once complete it will ask you to install the game. This file stays on your computer and you can move it where you want or install it without internet access. This is like the hardcopy of your game. It is yours(steam would never allow this).

Actually, I found a very easy solution. After doing a little searching (thanks to your suggestion), when clicking on the down tab for my MM6 (which is already installed), there was "Settings". When choosing Settings, I could uncheck "Automatically update to newest version".

So it should now not download the newest updates for the game and therefore I should be fine (I would think).

That is wonderful!