I don't know of any, but if it were me I'd make a copy of the document. Then remove a feature from the copied doc and test it. Remove another feature and test. Repeat until the content controls work properly.
We've done this and found it is the Table of Contents blocking the content controls from being updated. The table of contents is a business requirement so has to be in the document.
If you've solved the problem it is a good idea to mark an answer correct. That will help future users that come across the same issue.
I had the following response from support:
We are aware the Update Document action fails to update the document where there is a Table of Contents involved.
We have replicated this issue with SharePoint Designer and can confirm the issue is also present there. Unfortunately, this appears to be a limitation of the SharePoint platform which Nintex Workflows leverages to update a document. This is also confirmed by our Community member which can read here.
To address this matter, I will go ahead and create a public Knowledge Based article. Also it would be worthwhile placing a UserVoice request as this feature could potentially be implemented in future releases.
I have raised a request on uservoice please vote it up:
https://nintex.uservoice.com/forums/229405-1-nintex-workflow-for-sharepoint/suggestions/32809591-support-update-document-with-table-of-contents
update document