That was excellent to keep backups. And, right, C:\Windows.old has been skimpy since 1803.
(1) Did you have a file or folder on the Desktop greater than 5 GB (i.e., OneDrive default capacity)?
(2) Was anything moved to "C:\Users<Username>\OneDrive\Desktop"?
My theory is that the 1809 upgrade decided to "protect" the Desktop, Pictures, & Documents contents by moving them from "C:\Users<Username>" to same named folders in OneDrive. But, if there was a file greater than would fit
That setting is at...
(1) Right-click the OneDrive icon in the Tray, & click Settings. (Wait a tad for it to show.)
(2) At the Auto Save tab, click Update Folders.


Good guess and sound logic, but given the unique folder redirection established, OneDrive sync is not supported, so no -- nothing in there, no Auto-Save established, and no large files were stored.:

Just a (selective) wipe, so it seems, of my (non-folder redirected) C:\users\rcurtis\desktop. Certainly will be interesting to see if MSFT can expound on any semblance of logic as to what/when/why files are deleted...
... but something tells me we'll continue to wonder...
And no, I can't setup protection on any of those folders given folder redirection that is in effect. And I never used this function under 1803. Good thought by BarryG_961,
but storage sense was not enabled and I don't do any syncing with OneDrive -- just selective (manual) copies. Given I had a backup from 3 days prior and restored my deleted files, the largest file in that wiped folder is a ~290MB zip file. All the other
items in there are under 5MB. The other 'special' folders were unaffected -- no data lost from Pictures, Videos, or Documents - just C:\Users\rcurtis\desktop (a simple folder named like a 'special folder' but not a special folder.
None of the other exceptions noted in the OneDrive sync articles you noted come into play - other than the 2nd bullet under "Fix
problems with folder protection" given the aforementioned folder redirection (redirected and sync'd to a network share which is likely why none of my 'special folders' were affected. The C:\users\rcurtis\desktop folder that was wiped was not my
actual desktop (i.e. the 'special folder'), it's just a named folder I created and named it desktop. My actual 'desktop' is one of the redirected folders and was not impacted.
Based on some other posts on this forum, I ran an exhaustive check of all folders (nothing hidden) and there was no hint of any of my wiped files, and no hint of any other 'Desktop' folder out there in some rogue, MS created folder, or even Windows.old -- which
is where MSFT should be dumping anything it touches for this upgrade. And given the recent post by jjo1FF regarding
a true 'upgrade' vs. clean install, this was truly an upgrade leveraging the Windows Updater applet -- as I have done in the past with previous Win10 Creator Builds.
Despite having my files from my imaged drive backup, this is still deplorable -- MSFT should NEVER be touching personal data/folders/files, unless, after prompting and warning during a true 'clean install'. I would love to understand the logic as to why,
but sadly, this will be yet another perplexing head-scratcher and a prime example of poor QA testing with UX in mind.