Dear kupadhyaya,
Good day! Thank you for posting to Microsoft Community. We are happy to help you.
As per your description, please don’t worry, we can work together to narrow down and resolve the situation.
As you mentioned, "I downloaded a word document from SharePoint, which have tracking change enabled for audit purpose" instead of download Word document file from SharePoint online document library, you may open you Word document in Word for web (online) first and then click on "Open in app " to open your Word document in Word desktop client app then check the outcomes.
If above doesn't work, then the specific "Error! Hyperlink reference not found" message seems to be generally we cannot really rely on a result to display correctly as long as Track Changes is activated.
If you are not going to keep track changes in effect, if possible, please Turn off Track Changes before updating or make change to any of the hyperlink to avoid this error.
Your understanding and patience will be highly appreciated. I hope that you are keeping safe and well!
Sincerely,
Waqas Muhammad
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