I suspect that you are shutting down NinjaTrader by right clicking on the NinjaTrader program group within the Windows Task Bar and selecting 'Close Window'. When NinjaTrader is shut down by Windows in this way the operating system will first close all open windows - NinjaTrader would then prompt you to save workspace changes. If workspace changes are saved at this point a blank workspace would be saved as Windows has already closed all other open windows.
To avoid this issue moving forward, shut NinjaTrader down using the File > Exit command within the Control Center.
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