I am tested the below approach in Project 2010 and hope it applies to Project 2013 too
1. Exported task details that includes Unique Id and % Complete to Excel workbook
2. Updated the % complete in Excel workbook
3. Made sure default task mode is Auto Schedule, otherwise during merge Project is unable to calculate and update Actual Start, Actual Finish and other tracking fields
4. Import the Excel workbook using Merge option.
5. Since you have exported and importing the same file, the field mapping will be preset
6. Complete the wizard, and you should see % complete updated in Project file