Here is the code I have got working for opening and closing the server after a pause, import it into MS VS C++ after creating and setting up the project.

Code:
// SimConnectServer.cpp : Defines the entry point for the console application.
//Opens a connection to the server for 9000 ms, reports that the connection is alive
//and then closes the connection again.
//Written by MechDave using SDK Samples Open and Close as a code base.

#include 
#include 
#include 
#include 

#include "SimConnect.h"

HANDLE  hSimConnect = NULL;


void Connect()
{
    HRESULT hr;
	if (hSimConnect == NULL)
	{
		printf("Requesting a SimConnect connection");
		hr = SimConnect_Open(&hSimConnect,"Connect to Server for 9000 ms",NULL,0,0,SIMCONNECT_OPEN_CONFIGINDEX_LOCAL );
		if (hr != S_OK)
		{
			//FSX may be inactive
			printf("\nError %d", hr);
		}
		else
		{
			//Connection with FSX initialised
			printf("\nConnection request being processed (%d)", hSimConnect);
			//When connection process complete, an OPEN message will be recieved.
		}
	}
}

void Disconnect()
{
	HRESULT hr;
	hr = SimConnect_Close(hSimConnect); 
	printf("\nDisconnected from Flight Simulator");
    if (hr != S_OK)
	{
		printf("\nFailed to connect to Flight Simulator");
	}
	else
	{
		printf("Disconnection Sucessful");
	}
}

int __cdecl _tmain(int argc, _TCHAR* argv[])
{
	Connect();
	Sleep(9000);
	Disconnect();

    return 0;
}