Tim:
> > I wonder if you ended up with two /boots at some stage?  With the newer
> > kernels, etc, installed into the currently unseen one.
> > 
> > Do you have an unmounted /boot partition?

Andras Simon:
> How do I check? mount | grep boot
> returns
> /dev/sda1 on /boot type ext4
> /dev/sda2 on /boot/efi type vfat

They're the "/boot" (and its efi friend) that you're currently using. 
Compare that with your /etc/fstab file, see if they match.

And look at the output from lsblk (also looking for more than one /boot
partition).  It's also possible that you created a different /boot
partition than the one currently mounted.

You'd need to boot from some other media to see if there's a /boot
directory inside of / with some files in it.  While there can be a
/boot directory, you wouldn't want any files that you needed inside it
*if* you're going to mount a partition over the top of it.

> > Did you mount a /boot partition over a /boot directory?

> I didn't (manually/intentionally).

Normally, an installation will use a /boot partition mounted onto a
/boot directory, and all its files will be in the partition.  It is
possible to create a system that doesn't use a separate boot partition,
and it'll use a /boot directory, but (as far as I know) requires a
deliberate act.  And still requires an efi partition.

I should have asked first, but when you said you upgraded the OS, did
you wipe the drive and start from new, or did you upgrade over the top
of the prior OS?
 
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