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It is indeed possible to hide empty fields in your notifications. However, this does require the use of the default notification:
Since the data table needs to be locked in order to use this feature, it is not possible to have this active with a modified email notification, only the default with all fields included. Once this feature is turned on, only the fields that have data entered will be included in the notification.
If you have any further questions, let us know and we will be happy to help.