If you are trying to publish the workbook to server from Tableau Desktop 2018.1 start from step 1. or if you are trying to publish from Desktop 10.5 skip the first step.
1. Keep the Connection 'Live' (Change to Live if it is an Extract) in 2018.1 and Downgrade the workbook to Tableau Version 10.5 using Export as version option in Files>Export as Version>10.5.
2. Open this in 10.5 , still keeping the live connection and use the same option to downgrade the workbook to version 10.4 or lower.
3. Open the workbook in the downgraded version and create an extract now. Since the desktop version is 10.4 or lower now the extract would be a .tde file.
4. The workbook can now be published to Server without the .hyper error.
This is not a very straight forward approach and also requires you to have all the versions of Tableau Desktop running on your system. But this works if upgrading server is not the option.