I'm just throwing a guess here.
iOS 8 introduced iCloud Drive. After updating iOS 8, my keyboard shortcuts had disappeared, but only till I didn't upgrade to iCloud Drive. After upgrading, all shortcuts reappeared. Again, this might be the possible solution and I am not sure.
CAUTION : In case you are upgrading to iCloud Drive, keep in mind that iCloud is NOT compatible with iCloud Drive. Your data stored on iCloud on one device cannot sync with a device which has data stored on iCloud Drive and vice-versa.
Also, in case you own a mac, you have to have OS X Yosemite to access data stored on iCloud Drive.