Hi girodassoc@neuralrasa.com,
As per my understanding u-boot won't be a part of OTA process. As it is the boot-loader which is dealing with changing the boot partitions after the OTA, if we change the boot-loader and it gets corrupted then there won't be any way to recover back. You can also verify the same in the android source for i.MX8M Mini at "./build/make/tools/releasetools/ota_from_target_files.py". Here, you can see there is an option kept with the name "--full_bootloader", however there is nothing implemented for this option.
So, your u-boot changes are not seen after an OTA. I would recommend not to do an OTA of boot-loader, as failure in this won't be able to recover back to working boot-loader.
Feel free to let us know if you have any further queries in this.
Regards,
Kunal