steelblueskies just posted that you can overwrite shards on existing crafted items to upgrade one part of the item without deconstructing the whole thing first. Please rep the linked post if you didn't already know this; I know I didn't, and for me this is a game-changer.
In the Options panel under Gameplay, there is a new checkbox, "Disable Crafting Overwrite Messages," that is unchecked by default. The description of this option is as follows:
If checked, the crafting item effect overwrite message will not display when you apply an effect that replaces an existing one, such as when a new prefix effect gets applied and the old one is 'overwritten' and replaced.
I haven't actually tested it yet; I immediately created this thread to shout this revelation to the mountaintops. heh. But the description of it clearly states you can overwrite shards, which rules.