Hi @jaski.tx
We erased the eMMC memory (How to Erase the eMMC Flash Memory (Linux) | Toradex Developer Center), and tried to boot up the board in recovery mode using Toradex Easy Installer 2.0b6-nightly and it worked this time, we have also successfully installed 3rd party image which contained u-boot that works for us and our custom image. Version 2.0b5 also boots up correctly now.
Thank you @jaski.tx and @marcel.tx for support.
Best regards.