Hi @dwjbosman
Any chance you could post the logs to begin with?
Also, have a look at this, even though it is not for mender-convert, I think it is informal.
In general, /boot is mounted as a separate partition. Have a look in fstab, to make sure if it is boot, or /uboot (I think it is /uboot/ in this case).
So, in short, everything written to the boot partition is kept, as it is a separate partition.
The rest of your questions I think I need a log to look further into