Dear Jon,
From your description, it seems that the file is created with Excel 2013. If yes, I’d like to confirm whether you create a link referencing to the Excel file created with Excel 2013 in a newly created Excel 2016 file, save the file on your local computer and the issue happens when you click on Update after opening the local file.
If yes, I’d like to confirm whether the issue occurs in the specific Excel 2013 file. If you copy the data from the Excel 2013 file to a newly created Excel 2016 file, re-add the link formula in a newly created Excel 2016 file, restart the computer and do a test, what’s the result?
Moreover, what formula are you using, could you upload some screenshots and some screenshots showing the issue in your environment? Please also upload a full screenshot of the Account page in the Excel 2016 application you are using for our reference. You can access the page via File>Account.
Note: Remove any private information before uploading the screenshots.
Best Regards,
Cliff