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Factory Pre-programming of NAND Flash parts

Other Parts Discussed in Thread: AM3352

We are getting ready to move into production on a custom AM3352 based board with NAND flash running Linux.
I've been told that the flash parts will need to be pre-programed prior to being soldered on the board.
This means that following files will need to be written to the flash by some flash programming house

MLO
u-boot.img
devicetree.dtb
zImage
rootfs.ubifs

Currently during development all of this gets done by u-boot and or Linux and bad sector management, ecc, partition layout etc is all handled by the software running on the device. 

For factory pre-programming parts the programming house will need to make sure that everything is written with the correct bad-block scheme, error correction algorithm, and partition layout. To me this seems like a tall order fraught with peril. 

This also seems like something others would have had to deal with, can anyone provide me with some tips or information on how this is typically done. 

Thanks, 
Matt S.