I used to be able to use multiple pens in Krita, not something I have done too much, I just got a new wacom art pen and tried but to my dismay, both pens use the same brush when I select a different preset for each they still use the last brush selected. I am using 4.4.8 on windows 10.
4.1.7 it worked, 4.2.9 it was no longer functioning.