Since the schnapps export inexplicably fails any (medkit) clone of the current installation bears the potential risk of reproducing the same issue with the clone.
Nonetheless, and since only schnapps cobbles a medkit package, you could either try to manually tar package everything on the /dev/mmcblk0p1 and copy/unpack that to another partition.
Or use low-level dd to make a clone of the current installation for running off a USB drive (or interior mSATA), steps are mentioned here