I have a simple SVG which uses a <use> to render two bikes.

I would like to change the position of the bikes, which I would expect to change the x and y attributes of the <use> element.

Whenever I drag the bikes around, Inkscape applies a transform (translate) instead of actually changing where the <use> is rendered.

How can I edit the co-ordinates of the <use>?

Every SVG is a text file describing graphical shapes. Inkscape could be described as text editor with a fancy interface.

For a single shape, select the clone and open Inkscape's XML editor [shift+ctrl+x]. If you want to change many clones, it will be quicker to open your SVG file in a text editor with regex. Use find and replace to move coordinates from the transform attribute to x and y attributes. From this...

    <use
       x="0"
       y="0"
       xlink:href="#path1"
       id="use2"
       transform="translate(16,32)" />

...to this. (The order of attributes inside the <use .... /> element doesn't matter.) 

    <use
       xlink:href="#path1"
       id="use2"
       x="16"
       y="32" />