By default, when you password-protect a document, the entire file including its metadata, is encrypted. When you save your changes to SharePoint, it is seen as a new document and all its metadata values will therefore be emptied.
There are other disadvantages to password-protected documents:
- You lose co-authoring capabilities
- You will not be able to open the document in Office on the web.
- SharePoint’s search engine will not be able to index the content and thereby you will not be able to search for them.
Our recommendation is therefore to not password-protect documents that are stored in SharePoint. Instead you use other methods to restrict access to sensitive documents, see this page: How can I set permissions on documents in SharePoint?.
A Group Policy can be applied so that password-protected documents’ metadata will not be encrypted (the documents’ content will however still be encrypted), so when applied, when you save your password-protected documents back to SharePoint, they will not loose their metadata. Depending on security requirements, this may be an acceptable solution. Details about this Group Policy are described here: Document metadata for password protected files must be protected.