I did some tests and I'm going to report my partial findings here @theJesuit.
So, I tried re-adding Cryo Engines & Kerbal Atomics, but the loading screen got stuck and I saw this error:
[EXC 03:45:01.584] NullReferenceException: Object reference not set to an instance of an object
SimpleBoiloff.ModuleCryoTank.GetInfo () (at <febaf0f23bb3405bb0d4697c2f4076b6>:0)
PartLoader.CompilePartInfo (AvailablePart newPartInfo, Part part) (at <39c0323fb6b449a4aaf3465c00ed3c8d>:0)
PartLoader+<CompileParts>d__56.MoveNext () (at <39c0323fb6b449a4aaf3465c00ed3c8d>:0)
UnityEngine.SetupCoroutine.InvokeMoveNext (System.Collections.IEnumerator enumerator, System.IntPtr returnValueAddress) (at <12e76cd50cc64cf19e759e981cb725af>:0)
UnityEngine.DebugLogHandler:LogException(Exception, Object)
ModuleManager.UnityLogHandle.InterceptLogHandler:LogException(Exception, Object)
UnityEngine.Debug:CallOverridenDebugHandler(Exception, Object)
Checking Cryo Engine source code I've found that the exception could be linked to a missing fuel resource (due to the GetInfo method) which Kerbal Atomics or Cryo Engines is looking for.
Digging further, I've found a MM patch in Near Future Exploration when CryoTanks is installed, referencing explicitly the LqdMethane resource. Since the error shown before is thrown right after a NFX part loading, I’m pretty sure this is the critical point.
https://github.com/post-kerbin-mining-corporation/NearFutureExploration/blob/c449ef790bb99b2aa8074b2deafe4bd13c0fa940/GameData/NearFutureExploration/Patches/NFExplorationCryoTanks.cfg
So I'm thinking the boiloff system may be related, or an order in the MM patches. I'll update you if I find something else, anyway I'm attaching my logs here in case they can be helpful: https://1drv.ms/u/s!AqQ0YW9so_5OgQ7QnLDxo61c9FuD?e=WrItcg