How to fix an APFS corruption?

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A few weeks ago, I copied some directories from an old external hard drive to my iMac. I ended up with a few corrupt files due to the bad state of this ancient hard drive.

I managed to delete them, but some remain.

At the beginning, I thought it was only a question of file permissions or character encoding, but surprisingly, it's not. I've read every single posts in stackoverflow about similar issues on other unix systems.

Here are some screenshots, you'll understand easily the issue.

That is my OS and the bad files :

Introduction

I can not delete anything, even after rewriting :

Can't delete or modify non existent file

I can not chmod. Chmod shows me some ghost files I didn't know existed.

Can't chmod. Where do these files come from ??

I can not chown either :

Can't chown either.

This is an encrypted APFS partition :

Encrypted partition

I can not run any Disk Utility repair because of this FS corruption (exit error code 8). This doesn't work either on my Mojave USB installer, same error code.

Disk Aid

I can not decrypt the partition using FireVault, it stays stuck at 0% forever.

I never saw anything like this. What do you think we should do ?

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