The solution was to find where the update file was located in order to apply it and then to dd 2 files in order to reboot the phone.
I had no idea where it was though I knew it contained the word "nightly". I could therefore make a search based on that:
adb shell
find | grep nightly
It showed the following path: /data/data/org.lineageos.updater/app_updates/lineage-14.1-20170131-nightly-mako-signed.zip.
I could therefore browse from the recovery mode to apply this update.
Edit: I saw the command
fastboot continuewould do the trick. I'll test it on my next update.
What I had found was to reinstall the whole system which was not an option for me. I finally felt lucky to find a proper solution without reinstalling my phone.
adb shell
dd if=/dev/zero of=/dev/block/platform/msm_sdcc.1/by-name/fota
dd if=/dev/zero of=/dev/block/platform/msm_sdcc.1/by-name/misc
reboot
Note it may take a few seconds for each command line to apply. The phone would then reboot normally, though the first boot would be slightly longer.
By vinyll on Feb. 4, 2017