Is your workbook a TWB or TWBX (packaged workbook)?
The following applies to TWBX:
In a packaged workbook, the data gets embedded in the workbook when it is saved, and stored in a temporary file when the workbook is opened. If you refresh the extract, it will update the temporary file — but if you don't save the workbook afterwards, the updated extract will not get "re-embedded" into the workbook. Next time you open the workbook, a new temporary file will be created based on what was embedded in the workbook the last time it was saved, so it will appear that the data reverted back.
I hope this shot in the dark helps.