Coil Upgrades

I'm on cycle 28 or so with seven coil upgrades against me because of poor decisions and not realizing that skipping the coil missions applied the negative effects. And it seems that I have skipped two at the same time, which has greatly affected my progress.

I understand that this is part of the game, but I definitely made poor decisions here. The most recent save I can find I have five coil upgrades, should I fight through it or reload a save? It would suck to have to go back I was having so much fun until this point lmao.