I have tried to upgrade the system from a few older images (also with DKMS drivers) and this kind of behaviour did not occur. The issue seems to be coupled with the filesystem write operation and the following sync (should be invoked by umount command in the script).
Moreover, the .inc file should be updated formerly within the upgrade process (as the step of unipi-common package postinst script).
Can you retry the whole process with a new uSD card? This kind of problems sometimes occurs on corrupted cards as the write operation is not fully synced in fact.