Non-incremential backup and data archiving

Duplicati is a backup tool and does not do file replication, you should not ever fiddle directly with the backuped data, if you do that, you will most probably break your backup. It’s also a continuous backup tool, removing old data according to the retention policy.

The idea of ‘a complete backup from time to time, and incremental between that’ (known as grand father / father / son policy) is not appropriate for a tool like Duplicati, it’s not your grandfather’s backup.

The advantage of Duplicati design is to allow for deduplication, saving quite some backup disk space.
The disadvantage of it is that you can’t manage the backup data yourself.

If a tool does not fit your use case, don’t use it, do not try to use it like another tool for another use case. If you buy an utility vehicle, and try to drive it like a sport car, you may end up missing a curve somewhere. And the reverse case, if you try to drive a sport car on rough territory, you may break it.