Lost allocated space on 3tb drive after w8.1 update

Recently built a PC for a friend. The hdd (new wd caviar green 3tb) only showed 2tb. Not sure why uefi bios w7 to w8.1 via updates, ivy bridge system… Anyway i used the acronis software wd supply to allocate the missing space. All good, UNTIL windows update ran and the new partition disappeared. No idea how to get it back?? Doesn’t show in disk management anymore, made me look a bit silly tbh. Rather annoying
help please

If the hard drive is not being recognized, try using another SATA cable or another SATA port to connect it. If the problem continues, then the hard drive would appear to be faulty. If the hard drive is recognized, backup all of your files and try formatting it using GPT instead of MBR from the Disk Management windows. 

http://technet.microsoft.com/library/cc725671.aspx

The hard drive is recognized. For some reason i think windows has put some system files in a small partition on the data drive. I’ve looked at it a bit more and the primary boot drive is the 3tb in bios but the OS is on a 250gb drive. Is it possible to move that partition as it won’t let me delete to try a new format in disk management.