I got rid of the work laptop since then and hadn't had any issues with my personal laptop. It's probably not possible to figure out what have happened at this point.

I have tried to remove /etc/kernel/cmdline.d/ file with rd.luks.uuid and to run clr-boot-manager update: the boot option disappeared. So the issues is consistently reproducible on one of my laptops (but not the other). The one having issues is a ThinkPad X1 with an NVMe drive and the one don't having the problem is a MacBook Pro with a PCIe SSD.

Not sure if it's important at all but on my work laptop (the one experiencing the issue) I'm running Solus Mate and on my personal (the one going smoothly through the update) I run Solus GNOME.

You can try to get more insights into what's going on by removing these boot options from the boot loader: quiet loglevel=3 splash systemd.show_status=false. You can do it from the boot manager selection screen by selection a version of Solus and pressing e.

Apparently the root cause in my case was the lack of space on ESP for a new kernel which caused clr-boot-manager trigger to fail and depmod trigger never being run.