In general, you do not have permission to delete the existing startup.exe. Because of this, attempting to overwrite the existing startup.exe would fail. In fact, attempting to delete the existing startup.exe also should fail as a measure to prevent the accidental deletion of this file. However, you do have permission to rename the "startup.exe" to something else, such as "startup2.exe". You can then delete the startup2.exe, and FTP transfer your new startup.exe into the ni-rt/startup folder.