Hi Jemma,
You don't have to be afraid for data loss. Time stamp-based DataSources will hold the last extraction time stamp. It will continue after the upgrade like before.
Please note that an upgrade of the SAP Source System can have more impact. E.g. it is a best practice to empty the RSA7 delta queues. In your case it is an SAP BW upgrade, so do not worry about data loss.
Best regards,
Sander