Hello,

In Preferences > Clones there is an option to relink clones when duplicating a group of objects. This feature does not take linked clones in account which I think would make sense. Is this a deliberate choice?

Probably not. You could file a bug report about it.

As a workaround, you can copy and paste in place. (But you need to group the linked offset and the original object first, otherwise you will run into a different bug!)

That's a great workaround, thank you sas!
I used to edit the xlink:href-attribute manually.