I wish there was a way to fix this issue automatically, alas it cannot be done. Here's the solution:
Solution

1. Use Move It and set filter to select only props, surfaces, and decals.
   
2. Then click on the prop painter button, and set color to white

If you'd like to know why this is happening, here's the explanation. With recent update to Move It, the original Prop Painter fails at the patching stage, and silently fails (This is due to it using Harmony version 1.2). But with the way Cities Skylines is coded, the original Prop Painter Loading and Saving codes are still alive, hence when you keep playing and saving the game, the colors are all saved to black, because the color buffer was never initialized by the original Prop Painter core codes, since its dead during the startup stage. Thus, when using this new mod, all props are turned black, because it reads the old data saved by original Prop Painter.

Now, you may ask why original Prop Painter doesn't turn props black? The answer is simple, and it is because original Prop Painter core codes are always dead when you play the game. Thus the game is just using the default codes to set color of props. You won't be able to recolor the props, nor are custom colors displayed anymore.