Well, with Pyramid, I use the same trick than I use with an Elektron set only : the multi map that permit you to change patterns instantaneously. So the problem doesn’t occurs.
But for that, Pyramid isn’t necessary. Can do that with any Elektron machine.
Here I give a very useful thread that permit me to understand multi map on A4, in 5 min.
http://www.elektronauts.com/t/multi-map-to-transpose-and-switch-patterns/4815
So you just have to program the change (a note) on the first set of new pattern that wI’ll make change the other Elektron gear.
Everything wil be at the right place at the right moment on different machines
Edit: thanks to LarsErik