Can confirm, two of my nodes disappear when I reform government, I tried with different civics to see if it was related to a specific one but seems to do it with all of them; version 3.11.1 however my game IS modded, nothing crazy just some extra music and ship designs from Endless space.
Not sure if sharing my save would help because of the mods and most importantly It's on the cloud so not sure how to get it
Can you double check if this occurs without using any mods?