Replace Motherboard without Reinstalling Windows
Boot Windows normally and then open Windows Registry Editor. To do that:

  1  Press “Windows”  + “R” keys to load the Run dialog box.
    Type “regedit” and press Enter.
 
2. Inside Windows Registry, navigate (from the left pane) to this key: *

HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\services\msahci

* Note: If you have Window 8, Windows 10 & Server 2012, then navigate to the “StorAHCI” key
(e.g. : “HKEY_LOCAL_MACHINE\Repair\ControlSet001\services\storahci”) , because in these Operating Systems the MSAHCI has been replaced by StorAHCI.
At the right pane double click at 'Start' DWORD value and change its value data to 0 (zero). Click OK when finish.
3 Now perform the same modification to this key:

HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\services\pciide
At the right pane double click at 'Start' DWORD value and change its value data to 0 (zero). Click OK when finish.

If you use RAID  (otherwise ignore this step) then you have to perform the same modification to this key:

HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\services\iaStorV
6. Close Registry editor.

That's it! Now you 're ready to continue with your computer upgrade. When done, enter you BIOS settings and specify the SATA mode (IDE-ATA, AHCI or RAID) according your needs or leave the default setting. Exit BIOS settings and start Windows. Windows should start without problems. and install the required hard disk controller drivers. When Windows finishes the driver installation, continue to install the rest device drivers for your new motherboard..
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here is how, in case someone else need it:
i downloaded all the motherboard's drivers and put them (unzipped) on a USB stick; then i used the Windows repair disk to access the command prompt and connected the usb stick; then i wrote and entered this command :
dism /image:C:\ /add-driver /driver:X:\ /recurse

(change C if you have Windows installed on another drive / change X with the letter of the Usb drive containing the drivers)

at the end of the process , restarting, the PC will finally boot correctly

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    Download drivers for your motherboard and unpack them onto a USB or CD-Drive (I used a USB)

    Create a Windows Repair USB/DVD for your version of Windows

    Boot your PC into the Repair Utility and run the repair on your Windows, when this fails use back to get yourself to a menu with a command prompt option on.

    Insert your USB/DVD with the drivers

    Hit command prompt and find your USB/DVD drive letter using:

    dir $DRIVE:\

where $DRIVE is a letter from C-Z (mine was E:\ for instance), eventually you will find the USB/DVD with the drivers on. Once that is done enter the following line:

dism /image:$WINDOWSDRIVE:\ /add-driver /Driver:$MEDIA:\ /recurse

where $WINDOWSDRIVE will be C (or perhaps D depending what HDD your Windows sits on) and $MEDIA will be the Drive letter of your USB/DVD with the drivers on.

This should successfully copy your new motherboard's drivers across to Windows. Boot your PC back into Windows, at this point it may fix itself. But if it doesn't (as in my case) then attempt to switch your SATA mode from AHCI to IDE in the BIOS and start using Last Known Configuration. This rectified the problem for me but if this doesn't work for you remember that the hard part is probably over and you are quite close to having your OS back.