@Andreas Eklöf
There is an option to download the signed documents and the Certificate of Completion (CoC) as a package. In DocuSign this is called “Combined” download and it will give you a single PDF with the merged documents, but I think you have already discovered that option.
Combined download works only with the standard electronic signature accounts, which do not have Standard Based Signatures (digital certificates for e.g. AES or QES) enabled. This is to avoid invalid documents, when merging the documents into a single PDF. As it is an account-wide setting, it will also prevent the combined download for non-SBS envelopes in the same account.
If you tick the checkbox “Combine all PDFs into a single file” and you see that the document selection changes and is grayed out, this is due to the above stated. The Certificate of Completion has been unchecked automatically. This explains why you only downloaded the document, which is still checked, but not the CoC, which has been automatically unchecked.
For documents with digital certificates, like AES or QES it is recommended to keep the files separately and download them as ZIP file by selecting “All” and not ticking the “Combine all PDFs into a single file” checkbox.
Merging the documents using a separate tool is not a good idea, as it will break the embedded certificates. Therefore, the resulting document is invalid, as it has been tampered with and looses it’s legally binding.