Any shorts that may occur on the Trill side shouldn't break anything, as all used pins are 3.3V safe and only 3.3V is going to the Trills ... that's of course unless there's some severe electrostatic discharge situation going on, but then I'd expect Trill to fail first and then the BeagleBone, but it doesn't make sense to me that the audio in (of the Mini) or the whole cape (of the Bela) would fail ...
So I am a bit puzzled here ... Are there any other voltages being provided anywhere?