berobispo

Figured it out, using pishrink, finally! It takes a while because 28 GB of empty space are being copied in the beginning, but anyhow ;-)
This is my procedure:
 
1) boot from "plain" armbian (#2, see above)
2) insert original SD card (#1, 32 GB) in reader
3) dd if=/dev/sd#1 of=/path/to/image.img
4) pishrink.sh /path/to/image.img
5)dd if=/path/to/image.img of=/dev/sd#3, #3 being the backup SD card, 16 GB
 
note: "#1", e.g. is "/dev/sda", not "/dev/sda1", since you need to do a block level copy of the device, not only the disk.

I received my new Odroid HC4 today and ran into the same problem. I used the recent armbian, but I booted into petitboot (with an attached display and keyboard), and erased the flash storage from there. This worked just fine! As far as I can tell, this has no downside when compared disabling petitboot via ssh, other than having to have a display and a keyboard.
 
@Igor: Thank you for providing armbian!!!

...installed the JMS Firmware upgrade to be on the safe side and it seems I did not have the current version. See output of smartctl -a /dev/sdb1 below:
 
=== START OF INFORMATION SECTION === Vendor: JMicron Product: Generic Revision: 3101 Compliance: SPC-4 User Capacity: 4,000,787,030,016 bytes [4.00 TB] Logical block size: 512 bytes Physical block size: 4096 bytes LU is fully provisioned Logical Unit id: 0x3001234567891234 Serial number: 0123456789ABCDEF Device type: disk Local Time is: Tue Jan 29 11:45:38 2019 UTC SMART support is: Unavailable - device lacks SMART capability. Serial Number has changed, still no luck getting through to the HDD...
 
EDIT: solved it! 
 
smartctl -a /dev/sdb1 gives the result pf the JMicron bridge,
smartctl -a /dev/sdb1 -d sat gives the results of the HDD.

...installed the JMS Firmware upgrade to be on the safe side and it seems I did not have the current version. See output of smartctl -a /dev/sdb1 below:
 
=== START OF INFORMATION SECTION === Vendor: JMicron Product: Generic Revision: 3101 Compliance: SPC-4 User Capacity: 4,000,787,030,016 bytes [4.00 TB] Logical block size: 512 bytes Physical block size: 4096 bytes LU is fully provisioned Logical Unit id: 0x3001234567891234 Serial number: 0123456789ABCDEF Device type: disk Local Time is: Tue Jan 29 11:45:38 2019 UTC SMART support is: Unavailable - device lacks SMART capability. Serial Number has changed, still no luck getting through to the HDD...
 
EDIT: solved it! 
 
smartctl -a /dev/sdb1 gives the result pf the JMicron bridge,
smartctl -a /dev/sdb1 -d sat gives the results of the HDD.