Okay, let me tell you my whole story to guide your search.
I had a perfectly functioning Windows / Ubuntu install, Windows on SSD and Ubuntu on HDD. I swapped the two by copying the partitions and everything broke down, I had to repair Windows by booting an iso and struggling for days with the efi partition to rebuild it (I had deleted it when playing with the partitions...), the bootable USB didn't detect my Windows - still doesn't - and I have to get through a step of mounting the partition with diskpart every time I use the USB to try and repair my install.
Anyway, after this, I had to do at least a dozen passes of dism/sfc's, from Win itself and from a bootable USB, to make it stable again. My user profile got corrupted and I couldn't find a way to repair it so I created a new user, and here we are. I can bet that my current problem is still related to the boot setup / efi partition, but all my searches online lead to nothing, and having only a student Microsoft account, I can't contact the official support, so here I am, in the hope that making that last step (upgrade Windows) to repair it completely :)
I ran another sfc and here is the CBS log file, but I'm pretty sure it is "normal". My problem is probably subtle (though I may be completely wrong) and I hope the trained eye of yours can spot the weird stuff in the logs. Thanks for helping.