I have the exact same problem on my Lenovo T440p where today I installed Windows 8.1 64bit (UEFI).
I have a Samsung 850 Pro 256GB SSD as my primary disk and a Hitachi 500GB hard disk on the ultrabay adapter.
The Hitachi hard disk disappears/reappears at each sleep/resume cycle.
I have the latest BIOS and all the latest device drivers installed, including the Intel Rapid Storage Technology driver.
Did you find a solution for your problem?
Thanks!