I know this is from forever ago, but incase anyone else has this problem – I had it too and found out why it might have been doing this.
Apparently when you create an audio keyframe null from a long audio track you need to wait a handful of seconds for it to process all the keyframes it’s creating. If you try to do anything (even if it’s not involved with the null, for example, saving your project) it will delete the null layer immediately.
tl;dr – give it a minute.
-Matt