Once you clone the OS, the boot time will be very slow as the UUID for the partitions and the GRUB bootloader would have changed.
- Run to show the efi boot orders:
efibootmgr -v
- Check where the Windows EFI Boot file (bootmgfw.efi) is located, delete the
000X
of Windows Boot Manger using efibootmgr - Now create a new "Windows Boot Manger". (Refer this answer: https://askubuntu.com/questions/747215/edit-efi-file-paths-for-windows-boot-manager-from-xubuntu-14-04)