Yesterday I faced a situation where all deployed software updates packages contents started to delete itself suddenly.
I can see that all packages from source package path are getting deleted. I was bit curious and tried few things but nothing worked. Luckily I had backups. So I restored the drive from backup.
Finally figured it out that one of colleague created a new software deployment package to root of the folder instead of creating it’s own folder.
This is normal SCCM behavior to delete all contents from the package path and download new files into it.
So as soon as I restored drive, I renamed the deploypackage folder or the root folder for DeployPackages. Then updated the required package to point to correct folder.
As you can see in the above folder, it is going to root folder that was causing the folder to delete all other deployed packages and then download just new one.
Hope you will find it informative.