We've had a similar problem: the same error appeared when opening the query file in Excel, but after clicking "OK" on the error message, the exported data was opened in Excel - missing one specific column.
When hiding the column from the SharePoint list view and exporting again, there was no error message.
We found that changing the column to optional and back again to mandatory fixed the bug. After this change on the column, the error message in Excel did not appear and also the column was correctly included in the export.