Hi,
You can't manually run a Microsoft Defender scan while Windows is in S mode because protection works automatically in the background. The message you're seeing isn't directly related to scanning. It can sometimes appear when Windows has pending updates that still need to be installed or completed after a restart. Until those updates are fully installed, some Microsoft Defender components may not be in sync, which can prevent the automated scan from running properly. Since you're using S mode, your device is already well protected because it only allows apps that have been verified through the Microsoft Store.