Excel – How to troubleshoot “Automatic update of links has been disabled”

Check out this KB article method 4:

Method 4:

Enable the automatic update for data connections or workbook links in the Trust Center To enable the automatic update for data connections or workbook links in the External Content section of the Trust Center, follow these steps:

Click the Microsoft Office Button, and then click Excel Options.
Click Trust Center.
Click Trust Center Settings.
Click External Content.
Click to select the following options, as appropriate for your situation:
    Prompt user about Data Connections
    Prompt user on automatic update for Workbook Links
Click OK to close the Trust Center dialog box.
Click OK to close the Excel Options dialog box.

You cannot and should not have objects or processes managed by the trust center automatically do anything. This is setting a bad precedent. Instead, you should set the workbooks to prompt the users to update every time they open the workbook. If the users are prompted, they will be reminded to update the links.

Additionally, you can take a look at this KB article

Depending on the volume of the data you are copying, this may not be a viable option but...

You could copy the formula text for all of the linked cell without the equals sign with minimal slowdown and, once everything is in place, use CONCATENATE or search and replace to add the equals sign to the beginning of all of those text strings then let it crank out all of those links at once.

Let's say all of the data is in a range adjacent to "NamedCellNumberOne" You could paste "C:\Some folder\someworkbook.xlsm'NamedCellNumberOne" in the first cell then drag the corner of the cursor to "fill series" as needed. Once that is done, search all instances of "C:\Some folder\" and replace them with "=C:\Some folder\" to create all the formulas at once.