My controller very frequently got disappeared from SA 2.2. If I accidentally saved the project after the controller being disappeared, my controller got permanently gone. In this case, I have to restore it from svn.
Any more info that you could provide us would be helpful.
There is currently an issue where if a merge conflict happens and the controller's metadata contents become "corrupted" it will throwaway this controller. We're looking into fixing this for the next patch release.
Thanks for reply, @aconran. I have a pretty big controller in one of my projects. What I observed was as such: there are a lot of warnings as I edit the controller, some of the warnings are incorrect, I'm pretty sure. So, what I do is to conduct a cmd+a(select all) -> cmd+x(clear) ->cmd+v(paste back), then the incorrect warnings will go. I did it a lot in 2.1. However, I found in 2.2, the controller almost always will disappear after I do the same thing. Please note the statements above are based on my observation, I haven't had a concrete procedure to reproduce this problem, yet.