I was able to get again functionality since I also backup separately the local job database. So I restored it to the date at which the main job was last functioning, and remotely deleted all dblock and dlist files following said date. I then repaired the database and jobs are now working again.
Hopefully I neither needed a database recreate, nor to start the job from scratch. I speculate the issue was due to crappy internet connection, and inability by Duplicati to handle this.
However, given this kind of issues in Duplicati, I find it crucial to have a separate backup of the local job database, and to disable the automatic compact feature (using --no-auto-compact). Can anybody confirm that, this way, remote dblock and dlist files are never modified again, unless manually requested? (Besides files affected by retention policy, of course)
(This is on beta 2.0.4.5)