In the view manager of the assembly, click "edit", "redefine" for the "No_thru_cuts" rep; then click on the "substitute" tab, pick "plate-1", click the "No_circle" rep and then click "Accept", then pick "Plate-2", click the "No_square" rep, click "Accept" and then click the green checkmark. Then it will save the way that you want.
One extra hint is to use the same rep for all parts, (ex. "No_cuts" rep), then you can select all of the parts at the same time and select the one rep to substitute.
Hope this helps,
Arnold
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