@aldras thanks so much for posting this!
I ran into a similar issue this weekend and just found this post after pulling my hair out the last 2 days trying to troubleshoot… (we’ve got a CAN controller hooked up to the SPI3 peripheral on the SparkFun Thing Plus - nRF9160 and after upgrading from v2.3.0 to v2.4.1 the CAN interface stopped working).
I ended up using @jaredwolff suggestion to add a board-specific overlay in the child_image/mcuboot/boards
directory that just deletes the w25q32jv
node from the devicetree for this board (we’re not currently using it):
/delete-node/ &w25q32jv;