I lost all my keyboard shortcuts on my iPhone 5s after upgrading to iOS 8. They still showed up on my iPad Air (iOS 8) and iMac (10.9.5). There were, however, massive sync problems, sometimes they would only flow from one device to all the others, sometimes from one device to only one of the other two, sometimes not at all.
I deleted all my shortcuts and started from scratch, deleting “~/Library/Application Support/Ubiquity”, ~/Library/Dictionaries” and “~/Library/Mobile Documents/com~apple~TextInput” from the iMac and KeyboardDomain from my iOS devices.
Rebooted everything a dozen times.
Toggled Documents & Data Sync off and on a dozen times too in all kinds of combination with rebooting and deleting the aforementioned files.
Everything always starts working and syncing fine for a very short while, but sooner or later one of my devices stops receiving new shortcuts as I re-add them.
I reboot that device and it catches up. I enter new shortcuts, and that device doesn’t get any new shortcuts. This time, a reboot doesn’t fix anything.
After using my devices for a while, I notice shortcuts are entirely gone from both the iPhone and iPad, but not from the iMac.
I even upgraded my iPhone 5s to a 6, and right off the bat it had issues with keyboard shortcut sync. I also setup my iPad as new, and same thing: right off the bat, sync issues with keyboard shortcuts.