Hi @matiaslao,
It's possible to use a flash programmer (external hardware) to write all of the partitions to the flash storage at once.
First, create the image: use the flash programmer to read and create a binary image of an Omega2 that's setup how you want it,
Then, write the image to other devices: use the flash programmer to write the image to other Omega2 devices.
This is similar to the cloning process described in the FAQs.
The key differences are:
Cloning
Flash Programmer
Use Linux to create partition image
Use a flash programmer (external) hardware to create an image of the flash
Clones only the overlay partition
Duplicates all partitions on the flash
Our recommendation
We recommend against using a flash programmer to write complete images to the flash.
For one thing, the factory (aka art) partition holds wifi radio configuration and MAC addresses that are programmed at the factory and are unique to each device.
If the factory partition is overwritten, you will need to boot the device (either into the bootloader or Linux) to, at minimum, write unique MAC addresses to the factory partition.
If you're already booting into Linux, then it makes sense to use the sysupgrade command to install a firmware image as @JeffZhou mentioned above.
This process will only update the firmware and kernel partitions, leaving the bootloader and factory partitions as they are.
As a second option, in case this isn't helpful since you need to "clone" the firmware setup of a device, we recommend looking at this FAQ post: https://community.onion.io/topic/4563/faq-is-it-possible-to-clone-the-firmware-running-on-an-omega2-device-and-copy-it-to-other-omega2-units
It doesn't overwrite the factory partition, but there are other trade-offs.