I did not use the alpha of BTT. The bug is very difficult to describe and I had very much luck for one moment to do this. I will Install the alpha, but eventually I do not have enough luck to report this a second time as detailed as now and it was the first time that BTT itself crashed after that problem. So far I killed the application and restarted Mojave to be sure that no problems consists in the OS.
The first time I remarked this after the latest BTT update, never before.
I am using Touchbar and keyboard modifications for one app and sometimes the normal touch bar disappeares while spamming keyboard-input to the application. Mostly I did not receive control back for the keyboard to close the application normally and therefore I had to kill the application as fast as possible. This time I had time to study the strange behaviour of BTT and created a litte Movie with my iPhone.
The normal Touch Bar layout (basic layout when the app starts) returnes when pressing CTRL. Without CTRL the normal MacOS Touchbar is visible. I have some buttons defined to be visible while pressing CMD, this still works as you can see on the movie (sadly I cannot make screenshots of the touch bar
MacBook Pro (15-inch, 2016)
Logitech MX Master with Unifiying Receiver
Version BTT 3.372