Let me tell you the steps I took to painfully ensure I was rid of everything. So far so good, I will update...
1. Disabled iCloud drive on all four devices. Upgraded to iOS 8.4 on all. Turned off iCloud backup.
2. Deleted all local backups from iTunes.
3. Manually backed up all four devices.
4. Went into iBackupBot and deleted the keyboard folder and sqlite file REGARDLESS of the situation, although all devices but one had more than two folders, two of them had six, one had three...one had two.
5. Restored all devices from the new backups without the extra folders.
6. Deleted all backups from iTunes, and manually backed up all devices AGAIN. Made sure they still had two or less folders (they did).
7. Manually deleted ALL shortcuts from all but three of the devices. Edited the shortcuts on my main device.
8. Hard rebooted all devices (all changes still saved), disabled data and turned back on, and turned on and off device, syncd device, and hard rebooted a few more times (all changes still saved).
9. Turned iCloud Drive back on for the main device and hard rebooted. All changes still saved.
10. Turned iCloud Drive back on for the other three devices and hard rebooted. All changes still saved. Three no shortcuts, one all approved shortcuts.
11. Realized other three devices were not receiving shortcuts from main device. Signed in and out of iCloud/iTunes on one device to try to trigger a sync from the main device. Triggered.
12. A large portion of zombie cuts that I deleted from the main device sync'd back with the full dictionary to the second device. Not all, but most. I gave up on this device and in frustration completely wiped it clean. Not sure if that will help if this is the device causing all the problems or not.
So there is definitely more to this than just a local backup.