Hi @Mihan,,
I think you may be at the point where you need to 'clear the desk' somewhat and confirm what works and what doesn't. It seems you have too many unknowns and that can make a situation like this very hard to diagnose especially if it's your first time around a new board or build.
iMXs have a manufacturing mode set by dip switches or links that must be used after the initial programming. By default - out of the factory - they are blank and automatically in manufacturing mode for ease of programming during production.
Set the switches to program the board after which set them to back to boot and run the board. In most cases, users will be setting them to program the eMMC and then to boot from eMMC.
uuu is the successor to MFGTool and is better, there's no messing around with that xml file! Like MFGTool you still have to flick those switches to program eMMC or nand. Also like MFGTool everything gets downloaded into your boards RAM to eventually program the board. To flash a board nothing must be ran from eMMC (or nand, sd card), therefore once connected uuu will download it's own version of u-boot and a kernel with a ramdisk, everything it needs to boot and run a basic Linux OS in RAM in that instance of use. Once uuu gets a basic OS running in RAM it will start to download and program the board's actual uboot, kernel, devicetree and FS. You can see why everything has to be off the silicon for a complete reflash..
So it looks like uuu is not getting one of the requirements above. Personally I haven't seen anyone passing uuu an old_image with the new_image, normally you'd wipe the board and program it with just the new image. I do appreciate there's probably times where something like this is required.
So, back to your board. Have a search on the ZLG website and forums to see if there is a downloadable wic image for your exact board and try that. Also search the site for uuu information specific to you board. Use those manufacturing switches.
You mentioned that you built a smaller Yocto image for you board, did Yocto have the exact machine type for your board or did you use a generic iMX6 build (PMIC, pheripherials, RAM, eMMC specs will differ)?
Are you actually trying to program eMMC or an SD card?
If an SD card, are you trying to program the SD card using uuu with the card installed into your board?
Cheers.