It does, when performing a disk-to-disk cloning. When restoring a partition from a file in a second partition (source), by default, Clonezilla will restore the bootloader that it saved when making an image of a partition, although it’s possible to tell it to only restore the partition and leave the MBR alone. Here’s more information on the relevant options: -t (default: enabled) Client does not restore the MBR (Master Boot Record): Do NOT restore the MBR (Mater Boot Record) when restoring image. If this option is set, you must make sure there is an existing MBR in the current restored harddisk. Default is Yes, ie. Clonezilla will restore the MBR (where “MBR” = “bootloader”) -t1 (default: disabled) Client restores the prebuilt MBR from syslinux (For Windows only): If this option is set, the MBR is overwritten by prebuilt one which chainloads Windows. Use this option if you have to restore Windows and make it bootable, but don’t have the original MBR or backup of it. -g (default: enabled