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I'm currently using DisplayFusion Pro for window location (not only). I don't know how this works when you disconnect and connect your monitor - I have three always.

I think, that you must close and reopen your apps to be re-arranged.

Edit: This is feature is available only in Pro version. - Information from comments.

homepage of DisplayFusion

The problem is that Windows applications don't really see multiple monitors. The window manager keeps track of window positions in reference to the Top-Left corner or your main display. I'm not aware of any commercial applications that do, but you could write an application in C# or even VB.NET that could write these values to a file and restore them later, but there would be no "trigger" for it. You'd have to tell the program when to store and retrieve the data manually.

Try this script, written for Excel. It stores the window positions in a sheet and restores them from there. You may have buttons on one of the sheets to run the store and restore macros, or shortcuts to VBS scripts that run the Excel macros, maybe with shortcut keys assigned. That way the Excel workbook can remain minimized. Of course something similar may be written in a compiled program.

Public Declare PtrSafe Function GetWindowPlacement Lib "user32" (ByVal hwnd As LongPtr, lpwndpl As WINDOWPLACEMENT) As Long

Public Declare PtrSafe Function SetWindowPlacement Lib "user32" (ByVal hwnd As LongPtr, lpwndpl As WINDOWPLACEMENT) As Long



Public Declare PtrSafe Function GetWindow Lib "user32.dll" (ByVal hwnd As Long, ByVal wCmd As Long) As Long



Public Declare PtrSafe Function GetWindowLong Lib "user32" Alias "GetWindowLongA" (ByVal hwnd As Long, ByVal nIndex As Long) As Long

Public Declare PtrSafe Function IsWindowVisible Lib "user32.dll" (ByVal hwnd As Long) As Boolean

Public Declare PtrSafe Function GetParent Lib "user32.dll" (ByVal hwnd As Long) As Long

Public Declare PtrSafe Function GetWindowText Lib "user32" Alias "GetWindowTextA" (ByVal hwnd As LongPtr, ByVal lpString As String, ByVal cch As LongPtr) As Long



Public Type POINTAPI

X As Long

Y As Long

End Type



Public Type RECT

Left As Long

Top As Long

Right As Long

Bottom As Long

End Type



Public Type WINDOWPLACEMENT

Length As Long

    flags As Long

    showCmd As Long

    MinPosition As POINTAPI

    MaxPosition As POINTAPI

    rcNormalPosition As RECT

End Type



Global Const gw_hwndnext = 2

Global Const fwp_startswith = 0

Global Const fwp_contains = 1

Global title As String

Global Visible As Boolean

Global RowCount

Public prog As String





Public Sub StoreActiveWindows()

    Dim hwndapp As Long

    Dim hwndmax As Long

    Dim nret As Long

    Dim WinFrm As WINDOWPLACEMENT

    Dim RectFrm As RECT



    PleaseWait.Show vbModeless

    DoEvents



    RowCount = 1

    hwndmax = findwindow(0&, 0&)

    Do Until hwndmax = 0

    hwndapp = findthiswindow(hwndmax)

    If hwndapp Then

        If title <> "CURRENT WINDOWS OPEN" And Visible Then

            rtn = GetWindowPlacement(hwndapp, WinFrm)



            RectFrm = WinFrm.rcNormalPosition



            FrmTop = RectFrm.Top

            FrmRight = RectFrm.Right

            FrmLeft = RectFrm.Left

            FrmBottom = RectFrm.Bottom

            Workbooks(Filename).Activate

            Workbooks(Filename).Sheets("Active Windows").Cells(RowCount, 1) = title

            Workbooks(Filename).Sheets("Active Windows").Cells(RowCount, 2) = hwndapp

            Workbooks(Filename).Sheets("Active Windows").Cells(RowCount, 3) = FrmTop

            Workbooks(Filename).Sheets("Active Windows").Cells(RowCount, 4) = FrmRight

            Workbooks(Filename).Sheets("Active Windows").Cells(RowCount, 5) = FrmLeft

            Workbooks(Filename).Sheets("Active Windows").Cells(RowCount, 6) = FrmBottom

            Workbooks(Filename).Sheets("Active Windows").Cells(RowCount, 7) = WinFrm.MaxPosition.X

            Workbooks(Filename).Sheets("Active Windows").Cells(RowCount, 8) = WinFrm.MaxPosition.Y

            Workbooks(Filename).Sheets("Active Windows").Cells(RowCount, 9) = WinFrm.MinPosition.X

            Workbooks(Filename).Sheets("Active Windows").Cells(RowCount, 10) = WinFrm.MinPosition.Y

            Workbooks(Filename).Sheets("Active Windows").Cells(RowCount, 11) = WinFrm.showCmd

            Workbooks(Filename).Sheets("Active Windows").Cells(RowCount, 12) = WinFrm.flags

            Workbooks(Filename).Sheets("Active Windows").Cells(RowCount, 13) = WinFrm.Length

            RowCount = RowCount + 1

        End If

    End If

    hwndmax = GetWindow(hwndmax, gw_hwndnext)

    Loop

            Workbooks(Filename).Sheets("Active Windows").Cells(RowCount, 1) = ""

            Workbooks(Filename).Sheets("Active Windows").Cells(RowCount, 2) = ""

            Workbooks(Filename).Sheets("Active Windows").Cells(RowCount, 3) = ""

            Workbooks(Filename).Sheets("Active Windows").Cells(RowCount, 4) = ""

            Workbooks(Filename).Sheets("Active Windows").Cells(RowCount, 5) = ""

            Workbooks(Filename).Sheets("Active Windows").Cells(RowCount, 6) = ""

            Workbooks(Filename).Sheets("Active Windows").Cells(RowCount, 7) = ""

            Workbooks(Filename).Sheets("Active Windows").Cells(RowCount, 8) = ""

            Workbooks(Filename).Sheets("Active Windows").Cells(RowCount, 9) = ""

            Workbooks(Filename).Sheets("Active Windows").Cells(RowCount, 10) = ""

            Workbooks(Filename).Sheets("Active Windows").Cells(RowCount, 11) = ""

            Workbooks(Filename).Sheets("Active Windows").Cells(RowCount, 12) = ""

            Workbooks(Filename).Sheets("Active Windows").Cells(RowCount, 13) = ""



    Unload PleaseWait



End Sub



Public Function findthiswindow(ByVal hwndtopmost As Long) As Long

    Dim hwndtmp As Long

    Dim nret As Long

    Dim titletmp As String



    'Get the first window

    hwndtmp = hwndtopmost



    If GetParent(hwndtmp) = 0 Then

        'Set its visibility

        If IsWindowVisible(hwndtmp) Then

            Visible = True

        Else

            Visible = False

        End If

        'Get its title

        titletmp = Space(256)

        nret = GetWindowText(hwndtmp, titletmp, Len(titletmp))

        If nret Then

            findthiswindow = hwndtmp

        End If

    End If



    If Visible Then

        title = titletmp & " - Visible"

        Else

        title = titletmp & " - Invisible"

        End If

        title = titletmp

        If titletmp <> "" Then



        'If title = "SETTINGS" Then

            HasNoOWner = Not (GetWindow(hwndtmp, 4))

            n = 1

        'End If



        If (UCase(Left(title, 15)) = "PROGRAM MANAGER" Or UCase(title) = "SETTINGS") Then

            n = 1

            title = ""

            findthiswindow = 0

        End If

    End If

End Function



Sub RestoreWindowsLocations()

    Dim WinFrm As WINDOWPLACEMENT

    Dim RectFrm As RECT



    PleaseWait.Show vbModeless

    DoEvents



    Workbooks(Filename).Activate



    RowCount = 1

    Do Until Workbooks(Filename).Sheets("Active Windows").Cells(RowCount, 1) = ""

        hwndapp = Workbooks(Filename).Sheets("Active Windows").Cells(RowCount, 2)

'       rtn = GetWindowPlacement(hwndapp, WinFrm)

        WinFrm.rcNormalPosition.Top = CLng(Workbooks(Filename).Sheets("Active Windows").Cells(RowCount, 3))

        WinFrm.rcNormalPosition.Right = CLng(Workbooks(Filename).Sheets("Active Windows").Cells(RowCount, 4))

        WinFrm.rcNormalPosition.Left = CLng(Workbooks(Filename).Sheets("Active Windows").Cells(RowCount, 5))

        WinFrm.rcNormalPosition.Bottom = CLng(Workbooks(Filename).Sheets("Active Windows").Cells(RowCount, 6))

        WinFrm.MaxPosition.X = CLng(Workbooks(Filename).Sheets("Active Windows").Cells(RowCount, 7))

        WinFrm.MaxPosition.Y = CLng(Workbooks(Filename).Sheets("Active Windows").Cells(RowCount, 8))

        WinFrm.MinPosition.X = CLng(Workbooks(Filename).Sheets("Active Windows").Cells(RowCount, 9))

        WinFrm.MinPosition.Y = CLng(Workbooks(Filename).Sheets("Active Windows").Cells(RowCount, 10))

        WinFrm.showCmd = CLng(Workbooks(Filename).Sheets("Active Windows").Cells(RowCount, 11))

        WinFrm.flags = CLng(Workbooks(Filename).Sheets("Active Windows").Cells(RowCount, 12))

        WinFrm.Length = CLng(Workbooks(Filename).Sheets("Active Windows").Cells(RowCount, 13))



        rtn = SetWindowPlacement(hwndapp, WinFrm)

        rtn = SetWindowPlacement(hwndapp, WinFrm)



        RowCount = RowCount + 1



    Loop

    Unload PleaseWait

End Sub

DISCLAIMER: I'm the creator of this tool.

I've created a little tool to rearrange windows on a traybar icon click.
You may compile it from source or ask to have a (portable) binary through the issues link.

It is hosted at Github: https://github.com/manutalcual/winredock

I would be glad to hear from you if you have suggestions.

EDIT: 2018/11/22

It is fully automated now.

I've used Stardock’s Fences before in a similar scenario:

Fences helps you organize your PC by automatically placing your
shortcuts and icons into resizable shaded areas on your desktop called
fences. Its many customization features are what make Fences the
world's most popular Windows desktop enhancement.

Alot of windows users had this issue, an application was developed and shared within the windows 7 forums as shown here:

http://www.sevenforums.com/free-developer-programs-projects/40916-shellfolderfix-manage-folder-window-positions-size.html#post396744 

There are instructions on the site which help and it should fix your issue.

This one was looking promising: https://github.com/adamsmith/WindowsLayoutSnapshot

Unfortunately in my case, when saving the layout on 3x 24" 1920x1200 monitors, changing to one laptop 1920x1080, and then going back to three and trying to restore layout, windows didn't really move to other monitors. But maybe for someone else on other setup it will work.