How did you go about dd’ing the flash? Did you do this from the running/mounted OS/rootfs on the eMMC?
We don’t generally recommend this approach for making a production Linux image. We provide support for building Linux images using an OpenEmbedded-core/Yocto Project build system.
However, if you would still like to image the flash on a module, I’d recommend booting an image from another media (e.g. SD card, USB stick, Network) such that the rootfs isn’t mounted while you dd it. You can then dd back to the flash in a similar manner (while booted from external media).
This can also be done from U-boot; however, because two separately issued commands are needed to first write from flash to memory and then to write from memory to external media (or vice versa), it must be done piece-wise since the flash is larger than the available memory.