You need Winclone Pro 4.2.2 or higher (currently 4.4) for "keep BCD" to work.
The option you are after is "-b noreplace"
e.g.

SCCM_BootCamp_PreStage.winclone/winclone_helper_tool --self-extract -b noreplace -p /dev/disk0s4

All options available on winclone_helper_tool (as of Winclone 4.4)

Usage: winclone_helper_tool [options]
 -h                 This message.
 -c, --create               Create image.  Requires -p -j -o options.
 -r, --restore              Restore image.  Requires -p, -j and one of the following:-o,-k,-g.
 -i, --ntfsvolumeinfo           Get information about NTFS partition.  Requires -p.
 -o, --imagedir IMAGEPATH       Path to image.  Example: ~/Desktop/MyImage.winclone.
 -d, --diskdevice DEVICE_PATH       Specify a path to device to use in other operations. Example: /dev/disk0.  UNUSED.  DISCOVERED FROM -p ARG
 -m, --mbrfile              Read Master Boot Record and output to STDOUT.  Requires -d.
 -u, --genericmbr               When writing out MBR, don't map GPT to MBR.  Write standard guard MBR
 -p, --ntfspartition NTFS_PARTITION Specify NTFS_PARTITION (eg /dev/disk0s4) to use in operations.
 -e, --removepagefile           Remove pagefile from NTFS partition.  Requires -j and -p.
 -b, --copybcd FILE         Copy BCD or boot.ini to file FILE.  Requires -j and -p.  If path is set to noreplace and self-extract is used, the BCD is not copied.
 -g, --getfromstdin         During restore, get compressed ntfsclone image from STDIN instead of file.  Requires -r.
 -z, --ntfsresize           Resize NTFS filesystem to fill entire partition.  Requires -p and -j.
 -t, --ntfspartitiontype        Get partition type from MBR partition table based on partition number and device.  Requires -a, -d and -j.
 -s, --shrinkdevice PARTITION_PATH  Shrink NTFS filesystem at PARTITION_PATH to a minimum size.  Requires -j.
 -f, --partitiontype PARTITION_TYPE Specify partition type for -x option.  Requires -x. Example: 7
 -a, --partitionid PARTITION_ID Specify partition ID required in other options.  NO LONGER USED.
 -x, --updatembr PATH_TO_MBR_FILE   updates Master Boot Record from PATH_TO_MBR_FILE.  Requires -d, -a, -f.
 -l, --setsuid PATHTOBINARY     Sets PATHTOBINARY to always run as administrator.  Only works if PATHTOBINARY is the same as this tool.
 -j, --ntfsprogspath PATH       Specify PATH to NTFSProgs folder e.g. /Applications/Winclone.app/Contents/Resources.
 -k, --diskimagedevice RESTORE_DEVICE   When restoring, restore to RESTORE_DEVICE (eg /dev/disk0s4) instead of an image.  Requires -r option.
 -n, --licensekey PREFERENCE_PATH   Path to Winclone preference that contains a license key.  Required for creating images.
 -y, --self-extract         Self-extract mode.  Automatically sets the restore (-r) and associated flags (see -r usage).  Requires -p for partition to restore to. Uses resources in the same location as this script.
 -q, --quiet                Quiet mode.  Don't ask for confirmation...Just do it.

Hi Roy,
This is Russell, who you've been working with at Twocanoes. I just realized that you're asking about preserving the BCD when imaging. The "-b noreplace" option pointed out by Kumarasinghe is correct. This flag is applied when restoring an image. The assumption is that you may have a custom BCD created specifically for restoring the image of a file system like WinPE. When imaging, the BCD is always retained. It is when restoring an image that the BCD may need to be created new (typically hard drive or system migrations) or retained, like for WinPE restores. The Winclone GUI provides a preference set to retain the BCD or not. The "-b noreplace" option is the command line equivalent. We will expand on the documentation for this feature in the winclone_helper_tool usage and our website. I can't speak to the contents of the Casper deployment scripts, but you should be able to include the winclone_helper_tool commands in your deployment plan. Get in touch if you need any help. rts support@twocanoes.com

Thanks Kumarasinghe and Russell for your reply,

Hi Kumarasinghe,

How do you incorporate script to deploy the winclone image if you are following the instruction.
https://twocanoes.com/winclone/support/using-jamf-casper-suite-and-winclone-pro-to-image-a-lab-of-dual-boot-macs

1.Do you use Casper bulit-in function to partition the drive ?
2.If i use the step above , I don't see how you can incorporate script to ask Casper to retain the BCD during imaging since Casper just put the image down.

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HI Russell,

Yes i am using a custom BCD. It may be a good idea to include in your documentation to have example script and deployment method to retain BCD since Twocanoes already wrote the white paper of using Casper as an deployment tools to image a winclone image.

I am using Altiris here and we are using WinPE here to do the Windows Deployment and i have to use WinPE and custom BCD.

By the way, there is no Casper deployment scripts provided by Casper. There is nothing to speak to the contents of the casper deployment scripts.

@malroy
We do not use the Casper built-in function to partition the drive or deploy Winclone image.
We use a custom script to partition and deploy our SCCM Prestage in a Winclone image to do dual-boot imaging.

Hi Roy,
Another option to consider is to create a self-contained installer package using Winclone Pro. Once you've manually tested restoring the WinPE image successfully, select the image file and select "make package". Once completed, right-click the package and select "show package contents", navigate to and open in a text editor the file (packagename).pkg/Contents/Resources/postflight. Scroll to the bottom and you'll find the command "./winclone_helper_tool" with flags specified. Edit this command to include the -b noreplace option to preserve the BCD during restore.

I'll write up a help document for the Support page on twocanoes.com on preparing an image with a custom BCD for deployment.

rts