When running fsdt live update I get a warning that my simulator is running. This is not true.
Sure P3D is still running, why you think it's not ? The Live Update is asking Windows if the simulator is still running, so it surely was, and that number is the process ID reported back by Windows. I assure you the Live Update hasn't made it up...
A common mistake, is to assume that, just because you don't see the icon in the Task bar, the simulator has quit. It hasn't, especially if you have many add-on, are short on RAM, or a combination of that, it might take a while AFTER you don't see the icon in the Taskbar, before the P3D process is REALLY closed, including releasing all locks to the opened files.
If the message doesn't go away, the sim might just be stuck in the background, which can be confirmed from in the "Details" tab of the Task Manager. You'll find a Prepar3d.exe with a PID showing the same number you saw in the Live Update.