I have come across the same issue. I play mine own set of mods, basically all the All the Overhaul Mods (ATOM) but taking out Space Exploration, while adding dangOreUs, plus a whole bunch of QoL.
I notice there's two path, in the native ATOM Version:
Spectro --> Atmospheric Condenser --> CO Laser --> Laser Mill --> Microtolerance
But after taking out SE (and also deactivated ChemistryForYou):
CO Laser --> Laser Mill --> Microtolerance --> Spectro --> Atm Condenser
--> meaning unlocks
So when ChemistryForYou try adding kr-atmosphere-condensation as a prerequisite for CO Laser, which is then needed to unlock kr-atmosphere-condensation creates a cyclic loop.
I've removed the dependency to get it to work. It can be found in recipe-modify.lua Line 89, hopefully someone will verify my approach, but based on me checking out the recipes in the recipe book, it should work. Perhaps this could be addressed in a future patch?