Well this is a first for me.

I started the server and all drive came up as unassigned.

I re-assigned them and all was well until I shut down to check if it would happen again and it did upon restart.

Flash starting to go maybe? It's been in use since 2009.

Going to try my backup flash.

Diagostics attached.

tower-diagnostics-20160319-1814.zip

First thing to do is put your flash drive on a Windows pc and run chkdsk.

No windows here but I can run Disk Utility (Mac)

Just tried an other flash and it's the same issue but I am using the contents of the 1st flash except with the key for the 2nd flash drive.

Just check the 1st with Disk Utility and it doesn't show any issues.

Ok fixed, I think.

Trashed the super.dat file and re-assigned drives.

Rebooted and it seems to stick.