Well, yes, if d5 and d7 are the keys for the corresponding custom properties. Note, the names "d5" and "d7" are generated on the fly when your graph is saved to GraphML. When you save the next time, your custom properties for coordinates might use different keys. The keys are defined at the start of the GraphML file in a <key attr.name="..." attr.type="double" for="node" id="..."> element. You need to find the <key> element whose attr.name attribute value matches the name of the corresponding custom property to determine the correct id.
Aside from setting the values of the data elements, I suggest updating the corresponding label texts as well. The <y:ShapeNode> element in each node should have several <y:NodeLabel ...>text</y:NodeLabel> child elements. Suppose your x-coordinate is in the second label and your y-coordinate is in the third label, then update the value for the second and third <y:NodeLabel> elements as well.
If you update only your d5/d7 data elements but not the <y:NodeLabel> elements, you can use yEd's properties mapper to update the appropriate label texts from your updated property values once you open the modified GraphML file in yEd again.