*UPDATE*
I have now spent the evening digging through debug.log, dmesg and BIOS. It seems there are several problems here:
1. When ever i start the machine from powered off, the drives don't spin up until the mvsas driver is loaded by xpenology. As it does this, it doesn't wait long enough for the disks to spin up and initialize (I found that SATA drives are slower to finish than SAS drives, this might be part of it?). And since XPEnology doesn't seem to work well with hot swap, it never detects the remaining drives. Hence the "configuration lost" message, since it detects disks missing. Is there any way of extending this timeout?
If I then reboot or reset the machine, everything is working after boot. No configuration is actually lost.
2. The SAS card in combination with the onboard SATA controller (total 8 + 6 = 14 possible drives) somehow crashes the disk handler on boot (general protection fault) as it reaches drive 13. The stack trace shows SetSCSIHostLedStatusBy9235GPIOandAHCISGPIO being the culprit. I have logs saved if anyone is interested.
I disabled the onboard SATA controller, and now the machine boots as it should and detects all eight drives.
I still need to test cold booting after doing all this, but the server is expanding a volume at the moment. I'll be back!