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There may be a way to use XML Editor to link the objects, but I don't know much about using XML. Someone else will need to address that.
But there may be a quick way to make the objects new, and linked from the start. Check out Edit menu > Tiled Clones. It may not work to position the clones (although of course I've seen game level editors that indeed could be made with a tiled clones array). How many different sizes are there? Unless you decide to try tiled clones to both create and position the clones, here how you could do it, just to create the squares. Leave all the tabs in Edit menu > Tiled Clones with default values (if they don't have default values, use Reset button). Then on the first tab (I think it's called Symmetry) make sure P1 Simple Translation is chosen from the top of dropdown menu. Then let's say you need 10 squares of a certain size. Just set 2 rows and 5 columns. Select the parent square, then click Create button. It will give you 2 rows and 5 columns of squares all that size, all clones, plus the parent square. You can locate the parent square later, but I like to set it aside anyway. Then do that for each different size square that you need.
Depending on your needs, you may be able to use Tiled Clones to position everything. I just don't know, based the the info you've provided so far. Here's the manual info on Tiled Clones
http://tavmjong.free.fr/INKSCAPE/MANUAL/html/Tiles.html, and tutorial
http://tavmjong.free.fr/INKSCAPE/MANUAL ... ttern.html. The tutoriaal doesn't sound like exactly what you're doing, but it still might help
