Despite Microsoft pulling the October 2018 Update for deleting files, Microsoft have released the first update to the 1809 update. The update KB4464330 fixes an issue with deleting users profiles which sounds very much like the issue causing the file deletion problem. I wonder if Microsoft will resume the rollout with this patch included?
The update takes the build to 17763.55
This update includes quality improvements. No new operating system features are being introduced in this update. Key changes include:
Addresses an issue where an incorrect timing calculation may prematurely delete user profiles on devices subject to the “Delete user profiles older than a specified number of day” group policy.
Security updates to Windows Kernel, Microsoft Graphics Component, Microsoft Scripting Engine, Internet Explorer, Windows Storage and Filesystems, Windows Linux, Windows Wireless Networking, Windows MSXML, the Microsoft JET Database Engine, Windows Peripherals, Microsoft Edge, Windows Media Player, and Internet Explorer.