If patch deployed successfully via Endpoint Central but after reboot the patch still listed in missing list, the patch got roll backed, this must be an Environmental Issue
You install all the new patches that are missing. But the newly installed patches are again found missing once the computer restarts. All the new patches that were installed previously would have got rolled back after the restart with the following error: "Failure Configuring Windows Update. Reverting Changes."
This happens when the operating system tries to roll back to the way Windows was before the update. The updates could fail due to the following reasons:
1. Disable Anti-virus temporarily and redeploy the failed patches
If your anti-virus program blocks or otherwise interferes with a program installation you may end up with a failed install. Hence almost all software installation programs now recommend that you turn off your anti-virus before the installation to avoid any potential errors.
2. Deploy Cleanup Patch
Search and Deploy the component store cleanup patch 105979 from supported patches list and then redeploy the failed patches. Refer the following Knowledge Base on troubleshooting errors in windows updates.