Game settings reset, won't go past 30 fps, data gone.

You can certainly keep spare copies of your modified graphicsrules and graphicscards files and replace the ones in Program Files whenever necessary. I wonder if their reverting to default form is due to a "repair game" rather than a system update (though I could certainly be wrong), but in the end it doesn't matter—the files can be swapped as often as you like, as long as the new ones work for you.

The reappearance of the tutorial sounds more like your options.ini file is getting reset, most likely due to a graphics card drivers update. This is pretty typical. It's easy enough to keep a copy of the options file too, and replace it whenever necessary.

Your fps limiter may get reset by a driver update too, or by an update for whatever tool you're using. If adjusting the max fps rate within that tool doesn't work, try deleting and recreating the profile for TS3 or TS3W.exe.

By the way, you can always duck out of the tutorial by entering Edit Town mode.

Thank you, I'll try this out.