Not sure why it doesn't appear, but you can use SA_removeAugment SA_fighterTimeflow to get rid of it, hopefully.
Anyway, a fix for that crash will release soon.
I have the exact same problem, and i can't remove any of the augments once i install them without commands, once i put them and get out of the interface and come back to it, it just shows it like the augment isn't applied but it actually is since the effects can be seen (+10% market access for exemple)
And when i click on the augment to try to maybe remove it, it just doesn't do anything.