I’m glad you got it working fine. There are some remaining questions which you can look into if you wish to.
So if it’s still the case that that’s /tmp/Duplicati and you use --tempdir but not TMPDIR, that should be mostly Duplicati temporary files, not SQLite (which seems odd given the error). On Options screen 5, do you have Remote volume size increased past its default 50 MB, or dblock-size or asynchronous-upload-limit set up? You should be able to watch dup-* files moving through there as the backup progresses and its files upload. Additionally, you should be able to keep a good eye on space usage there with df, as it’s got only one usage. You can keep a good eye on the backup’s uploads from tempdir at About → Show log → Live → Information.
What filesystem is /tmp in now (e.g. per df), and is current setup showing that, or is this a historical guess? Invisible files (not the same as ones that begin with a dot) are ones that are still open but have been deleted. There’s no contradiction there on Linux. Files aren’t actually deleted until last user closes. Until then they are just fine from the using program’s point of view. From a filesystem point of view, they still occupy space on it. Finding these can be done from lsof output, looking for files which are marked as (deleted) in result listing.
When you say “at the end of the backup process”, do you mean in final stages, or at actual end or beyond?
Programs can’t hold files open after they’re gone. If you think Duplicati held files, try shutting down Duplicati.