At the start of the game I got most of my production lines to go green (efficient). When you upgrade the Assemblers, cutters etc. all of the machines of that type already on the map upgrade immediately thereby messing up the existing production lines. When you upgrade, have a setting inside each machine to let you manually adjust the input/output. Not the ratios. So, if you've just upgraded the Assemblers, you can click on the assembler and flip the switch from 15+15 input 15 output to 30+30 input 30 output.