Preventing users from deleting organization repositories

You can prevent members from deleting or transferring repositories in organizations on your GitHub Enterprise Server appliance.

In the upper-right corner of any page, click .
In the left sidebar, click Enterprise.
In the enterprise account sidebar, click Policies.
Under " Policies", click Repositories.
Under "Repository deletion and transfer", review the information about changing the setting. Optionally, to view the setting's current configuration for all organizations in the enterprise account before enforcing the setting, click View your organizations' current configurations.
Under "Repository deletion and transfer", use the drop-down menu and choose a policy.