Thanks for offering to look into this.

I have created a sample contract document and linked excel file here Update your browser to use Google Drive, Docs, Sheets, Sites, Slides, and Forms - Google Drive Help

While the sample contract contains mostly lorem ipsum text (for confidentiality reasons), I have retained some clause and annexure references in the manner that I usually use them in contracts, these are all highlighted in yellow for easy reference. There is also a contents page since longer contracts will need them.

Details of the issue
In my base template, all the clause references are properly linked, so ctrl+click on the reference "Annexure C" in the main body of the text will bring me directly to Annexure C of the document. Even when I export this to PDF, the clause referencing and hyperlinking works.

However, after I complete the MailMerge process, these clause references no longer work, whether the output is in DOC/DOCX/PDF format. The table of contents seems to contain some hyperlinks but clicking on them does nothing (and the formatting of the table of contents changes). Each of the individual clause references are now static text and I cannot ctrl+click on them to bring me to the exact position in the document that they appear.

I could live without these clause references in a short contract, but unfortunately these are important for the longer contracts. Any help would be greatly appreciated, but no worries if it is not something that can be fixed. I will probably just have to go back to doing things the long way.