[Google Pixel 7 Pro] simplepinoi177:
This write-up should still be applicable to this thread's OP's problem; for anyone who comes into this thread seeking some possible solution/advice.

Great! Good to know...

*Now a disclaimer: You stated you are using a Pixel 6 even though this is a Pixel 7 Pro forum and the only Pixels I have experience with is the Pixel 2 XL & Pixel 5 and I am currently using the P7P; so while I am fairly certain all the advice I give should be applicable to your Pixel 6, I can't be 100% sure. So, keeping that in mind, if there is anything you, or anyone reading that has experience with the Pixel 6, sees that may be inaccurate, I hope you speak up and enlighten and/or you might need to transpose it to work on the Pixel 6; but I will try my best to make it applicable to your Pixel 6 -- case in point; I almost wrote this leading you to flash the init_boot partition when IIRC all Pixels before the Pixel 7's implement flashing the boot partition. In any case, be prepared that there may be hiccups or unforeseen (be me) issues that you may need to, after first seeking help here of course, turn to those in the Pixel 6 forum and/or the users who are more familiar with that device; but I am sure nothing I will advise will hard-brick your device and is fairly universal to Pixels that there should be no consequence where you can't access the bootloader or recovery mode and be able to fix anything bad that may have happened. So considered yourself warned...

Although there is a way to accomplish the aforementioned steps/goal using Windows Powershell, I am unfamiliar using it (and it does seem to have its own hiccups & random issues) and am going to direct using the regular ol' CMD (command prompt) as is even preferred by the creators of the very well-established guides roirraW "edor" ehT and Homeboy76. Also, I have never used Windows 11, but am hoping all of the things from Windows 10 I advise are still applicable...

Also, please excuse me if I retread on information you may (obviously) already know; I can only glean that you used Magisk's patch to inactive slot (after OTA) method instead of implementing Full Factory images to update, but state you are familiar with adb and fastboot commands (so that leads me to believe you know how to extract the stock boot.img, but maybe have never ran the flash-all script because you may only update using OTA's), so in the interest of not using up more time to see where exactly your experience is and tailor my advice to that, I am just going to start at the very basic/start and work my way up where you would hop along wherever you are familiar with. Also, it helps anyone else who is in the same boat who reads this but may be inexperienced...

So, in essence, I am going to be referencing badabing2003's post & template HERE to manually flash the Full Factory image to both slots & root.

Download the December (or latest, for anyone who might come upon this at a far later date) Full Factory image of your Pixel 6 to your computer. You can download it HERE; I would have given you the direct URL, but I am unsure whether you are using a Pixel 6 or Pixel 6 Pro. Also, download the latest platform-tools HERE (this is directly from Google's developer's site -- you'd be surprised how many people get it from the Android Studio or minimal-adb-and-fastboot and then wonder why they get into trouble).

Extract both .zip's;

PLEASE

extract them in a totally different location than one you may have used before -- preferably a root directory like C:\ or D:\ -- in the interest of not running into issues of using outdated platform-tools and/or "image not found" type errors (that are very frequent and numerous in the forum here because users fall into the trap of having multiple of these platform-tools folders).

Extract the boot.img (init_boot.img file for you Pixel 7 people) file from the image-whateverpixelcodenameyouhave-randomalphanumerics.zip (either go into the image .zip file or extract the whole thing into another folder if you must).

Connect your phone to your computer

Move the stock boot.img (init_boot.img for you Pixel 7 users) file to your phone.

Load Magisk on your phone (Install Magisk from the .apk from their Github if you are running stock and/or unrooted)

patch the boot.img (init_boot.img for you Pixel 7 users)

*for anyone not familiar with this process, jackuphill is already familiar with this process, but to anyone reading who is not, please refer to the plethora of rooting guides on your device's forum; I particularly suggest using roirraW "edor" ehT rooting guide if it's available for your device.

copy the magisk_patched-randomalphanumerics.img file (in your Downloads folder) to the platform-tools folder that has the adb.exe and fastboot.exe files in it.

Go back to the folder where you extracted the Full Factory image .zip files. Right-click the flash-all.bat file and click Edit -- there are two flash-all files, so you may need to check/enable "file name extensions" to find out which one is the .bat file.

remove ANY reference to "-w"; there will most likely be only one, but you don't want that anywhere in the script -- this is if you do

NOT

want to reset your device to start stock/fresh. Consider the W in "-w" stands for "Wipe". You, @jackuphill, stated that you do not have any data to save, so this may not apply to you if you wish to start fresh with your device.

where it says "fastboot flash bootloader..." & "fastboot flash radio...", I want you to input "--slot all" after fastboot so it looks like "fastboot --slot all flash bootloader..." & "fastboot --slot all flash radio..."

copy the image-whateverpixelcodenameyouhave-randomalphanumerics.zip

filename

& paste it in another place (another notepad text file, notes app, word document, etc.) in preparation for the next step

replace the

last

fastboot command ("fastboot update image....") with the following code:

fastboot --skip-reboot update image-whateverpixelcodenameyouhave-randomalphanumerics.zip
echo Switching active slot to the other ...
fastboot --set-active=other
echo rebooting to bootloader ...
fastboot reboot bootloader
ping -n 5 127.0.0.1 >nul
fastboot --skip-reboot update image-whateverpixelcodenameyouhave-randomalphanumerics.zip
echo rebooting to bootloader ...
fastboot reboot bootloader
ping -n 5 127.0.0.1 >nul
echo flashing Magisk patched image ...
fastboot --slot all flash boot magisk_patched_randomalphanumerics.img
echo rebooting to system ...
fastboot reboot

optional: I like to remove the last command of "exit" so it doesn't close the command prompt when the flash-all is finished...

In the end, it should look like something similar to my (please remember to keep in mind I am using a Pixel 7 Pro, so codenames & version #'s are different and I'm using init_boot) flash-all.bat script:

@ECHO OFF
:: Copyright 2012 The Android Open Source Project
::
:: Licensed under the Apache License, Version 2.0 (the "License");
:: you may not use this file except in compliance with the License.
:: You may obtain a copy of the License at
::
:: http://www.apache.org/licenses/LICENSE-2.0
::
:: Unless required by applicable law or agreed to in writing, software
:: distributed under the License is distributed on an "AS IS" BASIS,
:: WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
:: See the License for the specific language governing permissions and
:: limitations under the License.

PATH=%PATH%;"%SYSTEMROOT%\System32"
fastboot --slot all flash bootloader bootloader-cheetah-cloudripper-1.0-9231809.img
fastboot reboot-bootloader
ping -n 5 127.0.0.1 >nul
fastboot --slot all flash radio radio-cheetah-g5300g-220923-221028-b-9229469.img
fastboot reboot-bootloader
ping -n 5 127.0.0.1 >nul
fastboot --skip-reboot update image-cheetah-tq1a.221205.011.zip
echo Switching active slot to the other ...
fastboot --set-active=other
echo rebooting to bootloader ...
fastboot reboot bootloader
ping -n 5 127.0.0.1 >nul
fastboot --skip-reboot update image-cheetah-tq1a.221205.011.zip
echo rebooting to bootloader ...
fastboot reboot bootloader
ping -n 5 127.0.0.1 >nul
echo flashing Magisk patched image ...
fastboot --slot all flash init_boot magisk_patched-25200_LYxqV.img
echo rebooting to system ...
fastboot reboot

echo Press any key to exit...
pause >nul

exit & close the notepad (or wordpad if that's how Windows 11 does it, i'm guessing)

MAKING SURE

it asks & confirms to save changes to the file before closing.

Move all the files you extracted from the Full Factory .zip to the platform-tools folder that has the magisk_patched-randomalphanumerics.img file, adb.exe, and fastboot.exe files in it.

Activate the Run window (⊞Win + R), type CMD, check "Run as Administrator" if there is an option/box to check, and press Ctrl+Shift+Enter (just for good measure to make sure to run the command prompt as Administrator).

*some people may be familiar with merely opening the platform tools folder in Windows Explorer and typing cmd in the path name, but that does not ensure running the command prompt with elevated Administrator privileges and to potentially avoid issues of that nature, I prefer doing it this way...

navigate to the platform-tools folder

I suggest running the cd command like, for example cd "C:\platform-tools\" -- instead of cd'ing into each folder individually -- if you did extract it to my suggestion of the root folder; this is why I suggest it, because navigating to the default folders like Desktop or My Documents folder is a bit more convoluted. I myself know a little better and have my own dedicated folder in my D drive, so I have to direct my cd command to drive first by first typing "D:", then "cd "D:\Phone Stuff\Pixel 7 Pro\platform-tools\" (I usually just copy & paste folder name from the top of my window in explorer).

Many people who use Powershell instead may be familiar with merely drag & dropping the flash-all.bat file into the Powershell window. This section/explanation is in case you are one of those people and are not familiar with navigating in CMD.

type adb reboot bootloader . Hopefully, you have enabled USB debugging; but you may still have to watch your phone to authorize your computer to your phone -- if so, you will have to run the adb command again. When your phone is in bootloader/fastboot mode, type flash-all.bat and press Enter.

make sure you do

NOT

touch

ANYTHING

until it loads back into the OS. You shouldn't have to type anything further or press anything on your phone until the OS loads up. It will

frequently

reboot on its own between bootloader/fastboot mode and fastbootd mode.

hopefully nothing happens and no hiccups come up. But if it does and say something like "waiting for device" for longer than 5 minutes, it is safe to attempt to disconnect then reconnect the phone to your computer (this has worked for some people). And/Or you can manually close the command prompt, navigate to reboot to bootloader on your phone, and run the flash-all.bat command again (I had to do this randomly because I was running an timedout adb-server). But if it "craps out" at sending/writing sparse parts or "can't load partition" or something like that, this may not have worked out and may have soft-bricked the device and will have to do further more specific troubleshooting. But you definitely do not want to touch or stop it when it's in the middle of sending/writing sparse parts -- like some users earlier on have done because they might be unfamiliar with fastbootd mode and/or not seeing the output in the Pixel Flasher GUI.

*I'm not 100% sure if running a magisk patched boot image/partition will properly work and properly load up the set up process on a stock initial set up if you have opted to keep the "-w" intact (as I've never done it this way before [I only update without wiping]; I believe this should work in theory. Then again, this template is taken from updating using the Full Factory images flashing to both slots and re-applying root...). If it does not, you must go back to the flash-all.bat script, edit out & remove the lines

echo flashing Magisk patched image ...
fastboot --slot all flash boot magisk_patched_randomalphanumerics.img

save, close, and run the flash-all.bat from the bootloader mode once more -- if you can get into the OS, you can run the adb command, but if not, you can get there using button combinations. Then, only after setting up the phone, do you flash the magisk boot .img and install/load up Magisk.

This was a pretty extensive write-up, so I may have missed something; but I am hoping to God that I didn't. If I did, I hope it doesn't cause too much trouble and isn't too hard to remedy, and you can always come back here and I will work my hardest to rectify the mistake. Of course, if anything at all, I hope it all goes well and this works and helps...