I’m investigation why at boot something on the filesystem change
Which version of Yocto are you using?
There could be one thing that is causing problems, and that is that the checksum in the uefiimg does not match what ends up in the Mender Artifact. This I believe only exists on older branches, that is warrior is expected to work without any further actions.
But if you are on something older then warrior, you need to deploy an full image updates once after the uefiimg has been provisioned on the device (or booted in QEMU in you case). This is to align the checksum with the Mender Artifact content.
You can read more about this issue at the end of Robust delta update rootfs