I agree. I've had similar issues where a USB stick or external drive had suddenly rearranged my drive order.

I have in the past also had the strange issue where the system wouldn't boot and looking in the BIOS the drives were in the wrong order and the boot drive was not set as the first to boot from.

Something else to do just to make sure is change the BIOS coin battery. A failing battery can cause these issues too, although as you have realised the cause could be the eternal HDD it probably isn't that.