That sound very similar to the old patch browsing within Dim Pro issue (I think it was Dim Pro). You are happily browsing through the sounds then every dozen or so a horrendous sound emanates from the monitors/phones and Sonar craps the bed. I haven't had that happen since X1 (mind you I haven't done that type of repetitive patch loading with DP for a while either) and I haven't seen it brought up for a while but it does sound similar and it's making me wonder whether it's a RAM overload issue or something.
Mind you it's not a single pop. It's like a weird horrific swelling of noise THEN a loud "KAPRRRRAAAPP!"
Scared the pizzle out of me the first time it happened... hurt my ears too.
Edit... oh and Sonar would crash or at least white screen. The manifestation of tracks disappearing and what not sounds like a build up to a crash. X1 used to crash pretty danged hard on me, X2 would just freeze. X3 has only crashed once and it was because I was being an numbskull (pressing ctrl + z a million times instead of using the history).
Put a limiter on your Master bus (but remember it's there and turn it off while you are mixing) while your doing stuff you think might result in this. It'll protect your gear and ears... supposedly. Not sure if that kind of thing would bypass the master. It's just what someone recommended to me when I originally reported this.