Your game is saved! It is saved to the cookies on your computer. You can safely close your browser and shut down your computer. But if after saving game you quit to the main menu - you wipe this save. So don't go to main menu.
An alternative to managing multiple layouts for cores could be to have "dormant threads" for each lab tech that can be placed on the core anytime but are only active when the corresponding tech is on.
@Five_Four: The probabilities are calculated by adding each color's probability value, multiplying by various bonuses (e.g. chance upgrade), and comparing it to the probability costs of the colors. The apparent disconnect you see is because having multiples of a color is Paint provides a large bonus to probability value.
Two things: Please don't allow the game to replace a Palette cell while I'm trying to swap it with another cell, and make the paint tier chances separate instead of cumulative in the display.
Thank you, glad you liked it! I will :D