I have a Raspberry Pi 3 and a chisteraPi which uses SPI communication.
I have a similar problem, after upgrading to linux kernel 4.9.59-v7+, my chisteraPi doesn't work anymore.
I use lora_chistera program :
This program use RadioHead library.
With a raspberry not updated with linux kernel 4.9.35-v7+, chisteraPi works.
I can't tell if it's a problem from the kernel or from raspi-config...