Oh boy, ... I accidentally commented out the line that mounts /media/mmc/boot to /boot. So apt updated /boot on the harddrive (not on the mmc) and several other locations on the harddrive, like the modules directory.
After the reboot, I still had the old kernel/settings but on the harddrive everything was updated to match the new kernel... That won't work, of cause.
So I moved the new kernel and settings from /boot to /media/mmc/boot and everything is back to normal.
drscheme got a reaction from Igor in Missing modules.dep.bin file (Debian 7.9, kernel 4.1.6-sunxi)