I seem to have resolved the issue with a little help from Applecare, proceeding as follows:
1) Backup all of your iPad and/or iPhone data through iTunes;
2) click off the "Sync Apps" button in iTunes and perform a "clean" sync of the device (all third party apps will disappear, as well as iWork apps);
3) Connect to the Appstore on iPad/iPhone and download your apps back, STARTING WITH IWORK APPS;
4) Sync back again with iTunes.
After taking these steps, documents in the cloud appears to have resumed regular syncing with no deletions, I will keep everyone posted as to how this solution stands, however it seems to be a conflict between iWork apps and other third party apps. If true, it's hard to believe someone at Apple hasn't posted this workaround somewhere yet. If this workaround is only temporary, let's hope Apple fixes it soon.
But it's worth trying, no more deletes here!