I have found posts about this issue going back for years but no actual solutions. The file that holds the file explorer pin data keeps getting deleted and recreated. I've had users report this issue on various different builds of Windows 10, and I've also had it happen in Server 2016. I've gone through clearing file explorer history, I've unchecked the 2 boxes in 'Privacy' of the Explorer Folder options. I've manually deleted and had the file recreate, or I put back a copy of the file I had created. In the Server 2016 instance, this was a fresh install and started happening on multiple users. I even tried changing permissions on the file below, but within a couple days, the permissions were back to default and the user had no pins again. I tried disabling this scheduled task, \Microsoft\Windows\DiskCleanup\ SilentCleanup, but still lost pins.
"C:\Users\%username%\AppData\Roaming\Microsoft\Windows\Recent\AutomaticDestinations\f01b4d95cf55d32a.automaticDestinations-ms"
I posted this question on another MS forum and was suggested to post here instead. Previous post (https://answers.microsoft.com/en-us/windows/forum/windows_10-start-win_general/file-explorer-pins-keep-getting-deleted/d3737dbe-2c90-46ca-b955-d6aef57034fc).