When my cards level up in story mode, sometimes they get energy back and sometimes they don't. Most of the time, they don't unless I kill my app and reload it and that works less than 30% of the time.
Also, this is the kind of problem you can write out in many different ways and has a lot of annoying side-effects to player enjoyment. So, different people are writing out the problem in ways other people don't know how to search.