duplicate entry in boot manager

after cloning HDD to SSD and fixing the dreaded 0xc0000225 error (using this How can I repair the Windows 8 EFI Bootloader?) I have now two identical options while booting OS

Windows Server 2012 R2
Windows Server 2012 R2

and timeout is 30seconds. I checked startup and recovery settings dialog but there is only one entry there! I also changed the timeout there to 3 seconds, but upon reboot I still see two choices and timeout is still 30seconds... bcdedit shows this:

Windows Boot Manager
--------------------
identifier              {bootmgr}
device                  partition=\Device\HarddiskVolume1
path                    \EFI\MICROSOFT\BOOT\BOOTMGFW.EFI
description             Windows Boot Manager 
locale                  en-us 
inherit                 {globalsettings} 
bootshutdowndisabled    Yes 
default                 {default}
resumeobject            {00b840ac-0c93-11e5-bdea-941b40ff01bb}
displayorder            {default} 
bootsequence            {default} 
toolsdisplayorder       {memdiag}
timeout                 3

Windows Boot Loader
-------------------
identifier              {default}
device                  partition=C: 
path                    \windows\system32\winload.efi
description             Windows Server 2012 R2 
locale                  en-us 
inherit                 {bootloadersettings}
isolatedcontext         Yes 
allowedinmemorysettings 0x15000075
osdevice                partition=C: 
systemroot              \windows
resumeobject            {00b840ac-0c93-11e5-bdea-941b40ff01bb} 
nx                      OptOut
detecthal               Yes

EasyBCD shows this:

Default: Windows Server 2012 R2
Timeout: 3 seconds
EasyBCD Boot Device: C:\

Entry #1
Name: Windows Boot Manager 
BCD ID: {5ead7c38-0c9b-11e5-aa31-e928f8e12847}
Device: \Device\HarddiskVolume2
Bootloader Path: \EFI\MICROSOFT\BOOT\BOOTMGFW.EFI

Entry #2
Name: UEFI: Samsung D3 Station 0200 
BCD ID: {e51c0507-0cf7-11e5-80f6-806e6f6e6963}
Drive: E:\
Bootloader Path: 

Entry #3
Name: Windows Server 2012 R2
BCD ID: {default}
Drive: C:\
Bootloader Path: \windows\system32\winload.efi

So I am not sure if I can delete any of it. Seems like the duplication is caused by something else...

Get Visual BCD Editor.

The tool shows complete BCD in a structured way so you can decide easier what boot entry to delete.

Clicking on an entry in tree view shows all corresponding BCD elements on the right side of display window.

The relevant entry you want to keep should have its boot loader path on drive C: (if you did a normal install) -> "\Windows\System32\winload.efi"

Hint:

Using "mountvol z: /s" on command prompt you can map EFI system partition to drive z: and explore using one of the dialogs for editing paths in Visual BCD Editor.