I almost didn’t post this, partly because takes some specific steps to repro the problem, and it is likely something specific to my machine or with a specific plugin. But I CAN reproduce it every time (on my machine! 
), so I thought it might be worth submitting to see if anyone has any ideas:
The problem appears to only happen with newest Arturia’s Matrix-12 plugin (just released last month), and I can only repro the problem from Cantabile (not standalone). You will see why as I explain the steps:
I have a SetList that contains a Song containing a Rack that contains the 64-bit VST2 Matrix-12 V2 plugin. The first time I get to this Song, everything works perfectly. But if I leave that song and then return to it (regardless of whether there was 1 song or 10 songs loaded in the interim), I hear a fairly loud pop, and the Audio Port is dead. I can get it back by disabling and re-enabling the Audio Engine, but the problem happens again as soon as I switch to this same song. (This is why I can only repro the problem from Cantabile, because I don’t have another host application with the capability of switching between songs and plugins on the fly.)
It does not matter which audio driver I use (I tried the ASIO driver from Focusrite, ASIO4All, and the WASAPI driver). The patch selected within Matrix-12 also has no effect. I do not experience this with the 32-bit version of the Matrix-12 V2 plugin (using JBridge), so that is my workaround for now. I also do not experience this with any other plugin (including the other 64-bit Arturia VSTs).