This situation seems rather straightforward, there's not much more to explain.
Our end user's pdf thats in question is a larger file, that may have been created out of multiple smaller pdfs but is now one file.
The bookmarks are all still there when opened in DC, however they fail to operate as they did in XI.
They do not have Reader installed and so, could not see if they are functional in that application but its doubtful.
Has anyone run into this situation before?
Sorry for the delayed response.
Would it be possible to share the pdf file with us to replicate the issue at our end? To share the file here in the forums, please refer to the steps given here: How to share a file using Adobe Document Cloud
Also, let us know Acrobat version and the operating system installed on the user's machine. To check the version: Identify the product and its version for Acrobat and Reader DC