How can I backup the storage of an Android phone connected via USB?

This probably has a lot of challenges, but here are some ideas to find a clearer yes/no status:

Can you see folders and files that you want? If so, can you right-click to get the path for them?
If there’s a path, you “might” be able to push it into Duplicati using Add a path directly box.

Before that, though, how well do typical Windows applications work when editing Android files?
Duplicati will want to open files and read through them (including attributes), write restores, etc.
Basically it needs to look like a largely normal file system, and I’m not sure you have enough…

Media Transfer Protocol is likely how you got in, but it’s a limited-ability special-purpose design.
Duplicati has no special support, but there’s a (possibly small) chance Windows allows enough.

Files Transmission using Media Transfer Protocol is one of the articles from a Windows backup
vendor that has MTP support in some of their products. I think File Explorer also supports MTP.
Google search also turned up “FreeFileSync supports MTP”, so maybe it can sync to Windows.

Basically, unless Duplicati can do it directly, you might be able to devise some indirect methods,
however I think there are other ways to backup Android that might be easier than using the PC.

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