I think I figured out how losing your Surface Paint happens. At least for me, this seems to be the cause. I don't know if Bloody Penguin has fixed this issue or not in his latest update. But here's what I have found out..

The Problem:
After working on your game, you do several saves,.. Game Saves; Auto Saves; and Quick Saves(F1). When you load them, they all are missing the Surfaces that you had painted. But in the game, you saw the painted areas just fine when you saved them.

FIX:
If you are going to change anything in Theme Mixer 2, Render It!, Relight, or other mods that mess with the game's color and lighting, save your game BEFORE you do those changes.

If you make changes to those mods, at some point it causes this problem. So I am now in the habit of Saving the game before I make those changes, and Exiting the game after I am finished with the changes, and load up my previous saves. The changes that you make in those mods are not stored in the game, so you don't have to save the game after making those changes.

ALSO, Make sure your Surface Painter Mod was not disabled in the Content Manager. I just had that happen, and I did not do it. AND you can always try the other Surface Painter Temporary Fix. AND make sure you have the Surface Painter's dependency mod, Extra Landscaping Tools

Hope this helps. Please post a comment if this works for you.