Hello, dexstar.

The energy body you experience during energy work is usually the etheric body, the energy field of your physical body. The energy body you typically experience at night during dreams and dream-like experience is usually the astral body - the body of feeling, sensation and emotion. Working on your chakras during an energy work session doesn't necessarily affect your astral body.

Since the astral body is the body you experience dreams in, doing affirmations before going to sleep might be helpful. Declare your intention to work on issues blocking energy flow in your dreams. You could start recording and interpreting your dreams. Take up a meditation practice. Some people also find therapy helpful (it's the emotional body, after all). A lot of spiritual practices are aimed at reestablishing flow in the astral body.

Cheers,
Oliver