Ah I was referencing for a LOS upgrade when all I need is a new kernel. I use Sultan and it detects Magisk and keeps it, so no loss in doing the kernel last after an OS update.According to OP's post, the kernel should be installed prior to TWRP and Magisk. That's the issue.
I have both of them already installed, and TWRP strangely installed in slot A whereas lineageOS and Magisk installed in slot B.
I've never noticed your condition with split recoveries on the two slots, but either way, you can fastboot boot twrp and flash twrp again if that is what you prefer, then just use either recovery to flash kernel and Magisk again as desired, over stock LOS.