“Thanks” for not reading the post I linked to, and executing the same commands that you already know won’t work 
Please take the trouble to actually read the post (I had to do it as well). If you have trouble, the post that starts with "I think I have found the solution. " may have the solution.
Please try those steps first, but do not reboot yet.
The output of lsblk and fdisk -l point out the cause of the trouble. It shouldn’t be a problem, but it seems some part of the system has trouble that your root filesystem is on /dev/sdb, and not coping with a full disk LVM on /dev/sda.
I’m quite sure that your server has been rebooted once in a while, so GRUB is installed.
Would you post the output of:
$ sudo cat /boot/grub/grub.cfg|grep /dev
I expect a line starting with linux and having something like root=/dev/sdb.... ; if it has /dev/sda there then your previous commands should have worked.
With that confirmed, install GRUB on /dev/sdb:
$ sudo grub-install /dev/sdb
With no errors, continue to tell dpkg/apt to use /dev/sdb:
$ sudo dpkg-reconfigure grub-pc
You have to check the output of the commands, or maybe change a bit here or there: it has been a long time since I had a system that booted off the second disk, or that had an MBR / grub-pc.
Solving this bit will bring your system back in a normal state and allow you to (finally) upgrade anything. That is good 
Having something go wrong here, will make your system not boot. In that case, you can’t boot, but the system itself is not broken: you’ll need a system rescue USB stick to repair GRUB in that case. Not bad per se, but annoying for sure 