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If anyone can offer any advice, I need some help trying to retrieve missing data from a SharePoint 2013 MySite/OneDrive for Business Site (On-Premise)

Backstory: We have users that have SharePoint 2013 Enterprise set-up with OneDrive and they use this religiously for sharing OneNote notebooks which are then locally synchronized with the OneNote 2016 desktop application. I received a call from a user that they were no longer able to synchronize their OneNote notebooks. After having a user log into OneDrive via SharePoint, I noticed that no files were contained in their OneDrive sites as if they were all deleted. This is for all users (roughly 40) and none of them have their notebooks anymore.

Notes:

  • Windows Updates are disabled on this server and no known infrastructure changes were made that would change availability, permissions, etc.
  • If I go into SQL Server Management Studio 2017 and navigate to that particular instance/database, the database is still 4.2GB. I attempted to restore this with Veeam prior to the date it happened (May 23rd) and OneDrive displayed a blank page, so I restored it to last night's backup (June 4th). IIS was restarted.
  • There is nothing in the Recycle Bin for the end user or the Site Collection Administrator.
  • I've dismounted and reattached the database with SharePoint Management Shell. This made no changes. IIS was restarted.

I've reviewed this article and when I query a user's library with the requested answer (and my relevant information/values), no data is returned. If anyone has any insight, I would greatly appreciate it.

EDIT: After reviewing permissions, the default "All Users (Windows)" and "Everyone" objects are allowed, which they were previously not. This leads me to believe that new sites were created in place of the old sites, but I'm not sure how to verify that or if that could happen.

EDIT 2: I attempted to use Get/Restore-SPDeletedSite as I found this article which could be a result of the issue, but the sites still technically exist; they're just missing data, so I can't restore the site over top. In the fear that deleting that site would cause the new "deleted site" to be the current site, I've refrained from deleting the sites.

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This answer worked for me, but I can't guarantee it will work for everyone as it involves deleting the current site and replacing it with an already-deleted site.

Get-SPDeletedSite https://sharepoint/site | Remove-SPSite -Confirm:$False
Restore-SPDeletedSite https://sharepoint/site Confirm:$False

This allowed me to restore the previously deleted sites. I have yet to identify how they got deleted, but this resolved my issue.

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