“Yes, BUT”. Duplicati by default saves all backup versions forever, so they just build up and occupy space. One can set retention rules to reduce them, but if it deletes the only version that had the short-lived file, it’s gone. There’s also no great UI to go searching for deleted files. If one knows the name, the find command can help. If one knows the timeframe when the file existed, and what folder it was in, one can look through old versions in search of it. Duplicati is not an archiver, like one might use for mandatory records retention. Beyond not having the right UI, forever is a long time, and programs designed for that may have provisions for data retrievals in some distant future. This is the sort of thing serious long-term archivers may consider.
Digital Preservation at the Library of Congress
Independent restore program can get your backup restored without any Duplicati code being runnable, but adding the ability to rummage around in old versions for the long-ago-deleted files would have to be added.
So the “yes” is that Duplicati’s intention is to allow restore of deleted files and specific old versions of files.
There are lots of “but …”. Duplicati is currently beta, and the idea of using a beta product for forever saves doesn’t fit well. Sometimes issues arise, and sometimes the solution is to delete a broken version, or start backup fresh. Either one risks your old version. I personally think Duplicati is better for short-term backups. There are also the UI issues mentioned. There have been some requests for UI enhancements to allow an easier view of versions all-at-once, or maybe even specially handling deleted files. None of that is done yet. Duplicati is also not a continuous backup, so if one backs up daily, a file that was created and deleted all in the same day might not be in any backup. I don’t know if that’s important, but I mention it just in case it is…
Basically I don’t personally think it’s currently a good fit for this use. You might prefer a special-purpose tool aimed at archiving (especially if there is any intention of deliberately deleting originals), from an established company with a well-proven product and special focus from design and planning aspects aimed at forever.