UPDATE: Wed Oct 10, 2018 . . . MS has now fixed the problem and it is safe to run the Oct-2018 update again!
Per Register Article:
“The problem appears to be that data stored in a user profile directory can be deleted. Permanently. Thus users who have cheerfully performed the update found themselves with a lot more disk space but none of their precious files.”
MS has advised users to call their support center and they will advise how to download additional MS tools designed to fix this problem. But in some cases, if the disk space has been over-written by the user, an additional tool using Linux media is recommended (MS now has this in their repos).