Although you probably didn’t mean it this way, that’s exactly what happens with the backup. A new version is not made (even if the backup runs) unless there is some change (such as a new file version) calling for that.
It appears that the original motivation for the author of this feature was genuinely to trim file versions to save space at the destination but to give a more configurable way than previously available, e.g. to thin over time.
Duplicati is oriented towards tracking views of every file in particular dated backup versions. A request heard (especially from CrashPlan users) is to have a different retention plan (such as forever) for deleted files and also to have a way to add them to the UI for restore. That would probably take a lot more code than this plan which does the usual delete, just with a more powerful selection ability, so I doubt it will happen anytime soon.
Although it’s not as pretty, finding briefly existing files can be done with The FIND command and all-versions. Having said that, Duplicati does mean to be a backup program not an archiver, and it also hasn’t left beta… Personally, I see it as great to save you from short term issues, but keeping your only copy forever is riskier.