Hi Jonathan Black,
Welcome to Microsoft Community.
*I've edited the original post to make the scenario easier to understand.*
Based on the information you have shared, it is understood that your device is experiencing issues related to Microsoft Defender.
It can truly be concern when specific viruses/trojans cannot be quarantined. This potentially reduces the security of the device.
Versions or malfunctions of application components may prevent them from functioning as intended.
These viruses should not have the ability to completely destroy the Defender component, and it is more likely that the Defender component was experiencing other problems prior to the issue.
Preparing for additional protection when a Windows reinstallation is not considered is indeed necessary, and multiple different brands of protection software have different focuses on their security capabilities.
We noticed another similar thread of yours mentioned additional In-place Upgrade related issues.
When In-place Upgrade does not offer the option to retain personal files, it usually indicates potential user profile corruption.
If possible, you can first try to transfer important data to a new user profile and recheck the options provided by the In-place Upgrade process. After performing a valid In-place Upgrade process, it will help you further decide whether you need to install additional protection tools. (Disclaimer: Please back up all your important data before performing it.)
Manage user accounts in Windows - Microsoft Support

Troubleshoot problems signing in to Windows - Microsoft Support

If I misunderstand your situation, feel free to correct me and share the information.
Best Regards,
Kyo.Y - MSFT | Microsoft Community Technical Support