So I find X3C to be a bit more stable, but this funny thing keeps happening: there seems to be an issue of me recording, say, a bass part, watching it be recorded,seeing it start a new take lane, stopping the recording, and voila! it has disappeared. Anyone else?
 
I also notice some real strange behavior on the CPU meter. This one project that I am working on was started on X2 last year. Eight tracks of audio: I have one instance of POD Farm2,  one of AMPEG SVT, and a few 64 bit compressors (t-racks). Addictive drums andSuperior Drummer both running doing separate things. Four busses with a single compressor, and the Master with Ozone 5 and ARC2. Nothing AT ALL major compared to a lot of my projects...and the CPU is spiking like a mofo.

Could this be the the per-project setting in Preferences > Project > Record "Allow Arm Changes During Playback/Record"? If it is set in the project try deselecting it.
 

Is the audio really gone or just the wave drawing?
If the latter then cleaning out your Picture Cache folder will make Sonar redraw those wave pics the next time that file gets loaded.

I appreciate that there are other issues but all things are not necessarily related. It's caught me before, thinking that I'd lost a recording but while the pic of the wave was gone the underlying file was still there.

Also take a look at some of the other threads here (use the search box above and enter "CPU"). This thread was done a short while ago and covers quite a few possibilities that you may want to check.