Question: Can Auto Color be used midway through a production or do you have to set up the colors from the beginning?
Answer:

You can start using Auto Color at any time, but it would be most useful and the least amount of hassle if you started at the beginning of the prodcution. Although to be very honest, if you’re already down the road in a production you might be better off just using Find and Replace ([Ctrl] + F), selecting “Color” in the “For” dropdown box, and switching out colors that way. 

Auto Color is something of abandonware at the moment, although now that I have some more experience within the studio environment I might update it to make it a more useful color and asset management tool when I have the time. We’ll see.