I was using mdadm to spawn multiple copies and also backups of a degraded mdadm Raid1 "array", off which I ran my system. After do-release-upgrade to 16.04 (and even just halfway to 15.04 IIRC) this system stops booting to emergency mode, which is not even accessible in ubuntu, as I cannot seem to directly log in as root, for it doesn't accept the password.
I was able to chroot in from another system and with an "update-initramfs -u -k all" and "update-grub2" was able to repair this issue for me, but after every "spawning" (recovery of the whole system to another raid device) both "degraded" copies are then non-bootable. Maybe just someone lead me to the changes section of mdadm since version v3.25 - when my habit using "mdadm mirroring RAID" was still supported. Regards