What's the deal? Losing root? Updating will too you a new boot.img , which is where the su binary is installed.
Sorry, just seeing so many Google Pixel XL owners with issues. Rooting, booting. I've been decrypted, rooted, running one custom rom after another. Testing, building. I install whatever su zip I have available when flashing. Froze my bootloader updates at April's ota , so no boot signing or loops. I'm rough on my Marlin, but can't say I have had any issues rooting, booting, etc. Im ocd , and stay on slot A, always flash a new room twice to stay there. Then vendors, reboot recovery, GAPPS and SuperSU. Profit$$