|The MBR will NOT be copied.|
The MBR will ONLY be copied if the ENTIRE drive is cloned, NOT a partition! When one clones a partition, only the partition is cloned! How could it be any other way? The MBR is NOT part of a partition, it is the first sector of the HDD, which is NOT part of ANY partition.
However, the "boot" sector/s are copied when a primary bootable partition is cloned. Thus all that is necessary to again make the partition bootable is to set the "active" bit in the in the partition table in the MBR.
Specifically, to make a primary partition active, set the byte (exclusive) at 1BE or 1CE or 1DE or 1EE to 80H. This is the first byte in the partition record for each entry in the partition table.