Yes, deleting the database would work on any system except ctrlX currently because you do not have direct access to the files of the HMI because it's all inside the app. As such you could of course extract the backup, open the SQLite file using e.g. SQLite Studio and deleting all of the associated data rows and then zip the project again and upload it. Please note that you have to ensure you actually delete the correct rows so this is at your own risk. Omitting the database from the ZIP file will simply not overwrite the existing data when uploading the HMI again.
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