No, currently Duplex doesn’t come with an automagic backup feature - it behaves like any other tool.
Hopefully, you didn’t accidentally wipe your data? 
In any case, this is a subject not just limited to Duplex, perhaps other script authors have thought about it too?
I’m pretty sure vV has done some research into this matter, but a quick search didn’t bring up any results.
Edit: Ah, found it. He’s added a “safe installer routine” to the Epic Arpeggiator which will preserve existing presets when updating.
But I would largely tend to agree with vV on the following (quoting from the tool page):
Until then, it’s a matter of “manually backing up stuff” or implementing various workarounds - much like the tools that save data inside sample-names.
Actually, that discussion (how to save tool data in a song) is quite similar - implement the functionality as a shared library, or as a native solution?