I have never seen this, but after multiple rebuilds of different versions of ESXi, I get the same errors when trying to do an upgrade of the exact same two volumes missing, I mean the same GUIDs each and every time. How is this possible, when I am wiping and re-installing from scratch can the same two VMFS volumes, having the same GUIDs, keep showing up. Even the installer is complaining that these are missing.
So, after the nuclear option, you know, nuke it from orbit, it is the only way to be sure, things are looking "normal". What I did is booted gParted and wiped all partitions on all disks, and created a partition with EXT4 on each disk and deleted, then repeated several times. Now, there's no way those GUID partitions could exist, and so far, things are looking better.