I am using the latest version of Magisk downloaded today.
I can try the boot dir
I am assuming the command you are telling me to run isSomething about the root patch seems to interfere with normal automatic OTAs. This happens to a lot of people. For some reason the system doesn't check for and download the update.
The update methods that work are described in the OP.
What version of Magisk are you using?
Try flashing the patched image to /boot.
Code:
fastboot flash boot <imagname>.img