This is getting frustrating, spent countless hours trying to figure this one out. I have a 4tb WD40EFRX. I have two of them in my system and one of the drives constantly goes missing.
Took the drive out and did a Drive test where I tested this drive for 2 days and not one bad sector or problem showed up. Thankfully I followed the sage advice here and do have a 40G backup drive in the system s did not lose anything. I have 7 other devices running, some single drive other raid. Only one that seems to go missing is the main drive where I store movies, TV and Music. When the drive is missing nothing can be done to bring it back while the system is up and running. Once the drive is missing, it takes multiple shutdown and restarts to bring it back. That is why I am suspecting a timing problem.
As I said, I thought the drive was bad but tested it for many hours, in another system and it looks good. OK so ruled out a bad drive. Then moved the SATA controller port from a installed card right to the motherboard, thinking maybe the raid port was bad and still going missing.
Questions:
Is it possible that the drive is not coming up fast enough and the system does not see it there ? is there a way to postpone the check on the drive and see if that stops it going missing?
What actually causes the system to think the drive isn't there? is it possible because I have 8 drives, is it taking too long to get them all? How do I know the drive "check" order and is there a way to change it ? FYI went from SATA 8 to SATA 5 and still doing it 
Can anyone point me in the right direction. I am spinning my wheels now ? Suggestions ?