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I've noticed that Onyx is pretty free with changing their formats and standards around.
Not scientific, but there are 186 classes in kReader that have "Migrat" in their name.
By rolling back you've made your scribbles/notes incompatible.
You've got an A/B device, don't you?
Are you sure that you replaced the correct slot?
Also, you can use an image tool (like my imgutil.exe) to take a peek at your boot.img and see if it's Magisk'ed.
Yeah, I know you said Linux.
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