1. Thank you for bringing this to my attention. This appears to be a bug in the logic when expanding a folder to queue the content, if the folder doesn't exist the status flag wasn't being updated to indicate an error occurred. This will be addressed in the next update.
2. The application must be run to process the transfer queue, it runs in the background and is minimized to the system tray area.
You can configure per site or schedule rules to automatically overwrite if the file exists.
From the task scheduler dialog > File Transfer Rules (Use existing rules or Use custom rules) when custom rules is selected the custom rules button will become enabled.
Our scheduling system is quite new and we haven't had much feedback from it, If you have any suggestions or requests please let me know and I will take them into consideration.
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