Can you send a signal to Windows Explorer to make it refresh the systray icons?

Take a look at this blog entry: REFRESHING THE TASKBAR NOTIFICATION AREA. I am using this code to refresh the system tray to get rid of orphaned icons and it works perfectly. The blog entry is very informative and gives a great explanation of the steps the author performed to discover his solution.

#define FW(x,y) FindWindowEx(x, NULL, y, L"")

void RefreshTaskbarNotificationArea()
{
    HWND hNotificationArea;
    RECT r;

    GetClientRect(
        hNotificationArea = FindWindowEx(
            FW(FW(FW(NULL, L"Shell_TrayWnd"), L"TrayNotifyWnd"), L"SysPager"),
            NULL,
            L"ToolbarWindow32",
            // L"Notification Area"), // Windows XP
            L"User Promoted Notification Area"), // Windows 7 and up
        &r);

    for (LONG x = 0; x < r.right; x += 5)
        for (LONG y = 0; y < r.bottom; y += 5)
            SendMessage(
                hNotificationArea,
                WM_MOUSEMOVE,
                0,
                (y << 16) + x);
}

Two important details for anyone using Louis's answer (from REFRESHING THE TASKBAR NOTIFICATION AREA) on Windows 7 or Windows 8:

First, as the answer was reflected to show, the window titled "Notification Area" in XP is now titled "User Promoted Notification Area" in Windows 7 (actually probably Vista) and up.

Second, this code does not clear icons that are currently hidden. These are contained in a separate window. Use the original code to refresh visible icons, and the following to refresh hidden icons.

//Hidden icons
GetClientRect(
    hNotificationArea = FindWindowEx(
        FW(NULL, L"NotifyIconOverflowWindow"),
        NULL,
        L"ToolbarWindow32",
        L"Overflow Notification Area"),
    &r);

for (LONG x = 0; x < r.right; x += 5)
    for (LONG y = 0; y < r.bottom; y += 5)
        SendMessage(
            hNotificationArea,
            WM_MOUSEMOVE,
            0,
            (y << 16) + x);

For anyone who just needs a utility to run to accomplish this, rather than code, I built a simple exe with this update: Refresh Notification Area

Include following code with yours to refresh System Tray.

public const int WM_PAINT = 0xF;
[DllImport("USER32.DLL")]
public static extern int SendMessage(IntPtr hwnd, int msg, int character,
                                     IntPtr lpsText);

Send WM_PAINT Message to paint System Tray which will refresh it.
SendMessage(traynotifywnd, WM_PAINT, 0, IntPtr.Zero);

As far as I know that isn't possible Gustavo - it's up to each application to put its notifyicon in the systray, and ensure it's kept in the right state.

You'll notice sometimes when explorer.exe crashes that certain icons don't reappear - this isn't because their process has crashed, simply that their application hasn't put the notifyicon in the systray when the new instance of explorer.exe started up. Once again, it's the application that's responsible.

Sorry not to have better news for you!