De acordo com este artigo no MSDN , as pastas de trabalho fazem referência à mesma tabela de links internos. A solução alternativa (não verificada) é abrir cada uma em uma instância separada do Excel.
Symptoms
If you open multiple Excel workbooks that all contain links to the same source workbook, and you choose not to update the links, the links in all of the workbooks will be updated to the values that are stored in the last workbook that was opened.
Cause
This behavior occurs because link information is stored in an internal link table. This link table is shared among all open workbooks in that instance of Excel. The most recently opened workbook provides the link table that is in memory at any specific time.
Workaround
To work around to this behavior, open the workbooks in different instances of Excel. As a result, each workbook maintains its own internal link table and stored values.