Hi,
Thank you for coming Microsoft Q&A.
Does the issue occur after upgrade? Or does the issue occur after you configured certificate and restart in Windows 10 20H2, and it will repeat appear during every restart?
There is a known issue which published in your system version build package November 10, 2020—KB4586781 (OS Builds 19041.630 and 19042.630) about certificate will removed after upgraded in a specific scenario.
System and user certificates might be lost when updating a device from Windows 10, version 1809 or later to a later version of Windows 10. Devices will only be impacted if they have already installed any Latest cumulative update (LCU) released September 16, 2020 or later and then proceed to update to a later version of Windows 10 from media or an installation source which does not have an LCU released October 13, 2020 or later integrated. This primarily happens when managed devices are updated using outdated bundles or media through an update management tool such as Windows Server Update Services (WSUS) or Microsoft Endpoint Configuration Manager. This might also happen when using outdated physical media or ISO images that do not have the latest updates integrated.
Note Devices using Windows Update for Business or that connect directly to Windows Update are not impacted. Any device connecting to Windows Update should always receive the latest versions of the feature update, including the latest LCU, without any extra steps.
We recommend to try the workaround steps in that link to rollback to previous system version and check if certificate will back to device.
To make sure you have enough time to perform action, we need to use DISM /Online /Set-OSUninstallWindow /Value:<days> command to extended available rollback time. The default time is 10 days. If you have not set the time, after 10 days, it is not able to rollback.
Here is a similar thread with your issue.
Windows 10 ,Feature Update to 1909, Certificates missing after
If I misunderstood your issue, please reply to us directly.
Bests,
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