Marc,

So far, the only factual data does not show any problem, and the only
input stating something is wrong is actually you saying that.

My previous piece of advice with sfill was to kinda force *all* the free
space to be allocated, then released... Kinda desperate measure, which
would indicate something *very* wrong with the ext4 filesystem you use
on that disk.

Before going further, I guess the problem shall factually be
demonstrated. Here is what I suggest:
1°) sudo du --block-size=512 -s /mount/point
2°) sudo find /mount/point -print0 | xargs -0 ls --block-size=512 -ds |
awk '{print $1}' | paste -sd+ | bc

This should compute the size of all resources without dereferencing
links. Make sure no supplemental mount is made inside the hierarchy
you're inspecting.
Hopefully results are the same.

Bernard (Beer) Rosset
https://rosset.net/