Just to clarify a couple of things, no one is restoring an earlier version of the file manually (in fact, no one even accesses the file via the SharePoint Site interface, they do it through the share link that I've generated) and there is no OneDrive sync client involved.

The version at 4:42pm lost all of these changes – it basically reverted Includes most of the changes that were made yesterday. I dug into the version history, and noticed that the However, last night, one of our users noticed that a significant number of her changes had been lost. Up until yesterday we thought we had put this problem behind us. So the suggestion was to have users access them through 'sign-in required' share links. Back then, we only noticed this issue with files that were shared via anonymous links. After 10+ hours of troubleshooting and talking to numerous Office 365 support agents, our best diagnosis was that the issue was caused by the SharePoint Online service degradation that was occurring at the time - it had something to do with 'public-facing SharePoint'. We first noticed that some of our changes were disappearing back in Feb this year. They make changes through their web browser ( Excel Online) 99% of the time - this is done so that multiple people can edit them at the same time. Users access these spreadsheets using 'sign-in required' share links that I have generated. We have a number of massive spreadsheets that are hosted on SharePoint Online. To be more precise, the Excel file seems to be reverting back to an earlier version (we have major versioning enabled).

Excel 2016 online