I have had the invisible aircraft phenomenon happen to me in two of Baumer's missions
the 12 v 12 spit v 109, and the 4v4 zeke v F4F
So I don't think it's dependent upon mission size. Also, I dont think that it's certain aircraft that are becoming invisible, as in the 4v4 I clearly remember all 4 bogeys going down, and I still had an invisible pursuer.
It's very very jarring, after flying AH for so long you come to accept certain truths, such as clear six = nobody will be shooting you from your six. Takes a little while to even get used to it.