I always flash EMMC first (no -R), then take battery out, then rootfs.

So for your suggestion, I did this if I understand it correctly:
_flash combined (no -R)
_continue flash vanilla (no -R)
_take battery out
_flash combined again

The result is still the same.

Can the battery be the cause anyhow? When I was playing around with rescueOS, I noticed sometime I got sudden shutdown. Moreover when I took battery out and put back in, the phone can't boot straight away. I had to adjust the battery position a bit (sliding over it back and forth). I think it may be somehow loose. But the battery is still functioning, so I really don't know what's wrong with it.