You can prevent a document from deletion through the Lock Document feature:
- To lock a document, right click on a document in Document Navigator (The selected mode should be View Mode) then select Lock Document. A locked document has a purple tag added. To unlock the document use the right click document menu and select Unlock Document
- To lock all documents within a specific content type, right click on the content type and select Lock Content Type. The locked purple tag will appear on the Content Type level. To unlock the content type, select Unlock Content Type from the right click menu. Similarly, you can lock/unlock Categories and Sub-Categories to prevent all included documents from deletion.