Board Thread:Questions and Answers/@comment-45.124.5.106-20171215145316/@comment-25669516-20180310120343

Adding to what the IP above me said (very nice and detailed explanation btw), you will not receive Shadow Energy when you upgrade items from shop or spend Energy to upgrade it in the equipment tab. You can only receive Shadow Energy when an equipment levels up via chests, booster packs or mission rewards.