SharePoint supports securing and restricting access to files using IRM / DRM / RMS. Similarly there is Azure Information Protection (AIP) and other document encryption services such as Oracle IRM. Third party software, including Muhimbi's PDF Conversion products, do not have the ability to open encrypted content. This behaviour is by design, once a document is secured using a DRM technology, only a known set of users should be able to access it.
As a result these kind of documents cannot be converted or manipulated in any way. If document manipulation (Conversion, watermarking, merging, splitting) is required and a DRM product is part of the picture, then make sure you manipulate the document BEFORE applying DRM.
If there is some flexibility in the project's requirement, then Muhimbi's PDF Conversion software can act as a 'DRM-light' solution as it comes with the ability to automatically apply user specific watermarks when a document is opened, and secure the document with a password at the same time. Details about this facility can be found on our website for SharePoint on-premise and SharePoint Online.