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On Running LabVIEW application as shell after Windows Logon

I have developed a LabVIEW shell application that will run after I have logged into my Windows 2000. I execute this application by modifying the registry value of Windows so that everytime the Windows is logged into, user can only access the LabVIEW shell without having control of desktop. I would like to know if constant modifying of registry (due to constant changing from LabVIEW shell back to Windows desktop and vice versa) would damage the registry or not. I also wonder if my shutdown/logged off function at my LabVIEW shell would cause corruption to my execution shell file because the shutdown function would just shutdown the system immediately. In other words, what are the "safety" features for this kind of
application and importantly is how to prevent file damaging or file corruption in the system?
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Constantly modifying the registry poses only the normal risk you run with the registry as a single point of failure for the entire operating system. Just make sure you back up on a regular basis if you think you're going to screw something up but otherwise, you should be fine if you are changing documented options.

I also don't think you really run the risk of corrupting your executable during shutdown... it is my understanding that if you had open files or something of that nature that needed saved, you could create an event structure with a case for application exit that would close those files when the OS tells your executable to shutdown.
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