When a Jedi performs 'The Art of The Small' they reduce in size to that of an atom. How does a Jedi remember to reassemble themselves cell by cell if atoms have no consciousness or memory?
According to The Art of the Small article on wookieepedia it reduces their "presence in the force", not their actual body, so there should be no need to reassemble. This is elaborated in the "Healing" subsection of the "Force-Sensitive Abilities" section of the book Jedi vs. Sith: The Essential Guide to the Force, which quotes a recording from a Jedi named Cilghal about a conversation with a Force-user called Vergere who used the technique of "making herself small":
I met with Vergere in her cell, where she had spent many hours being debriefed by Fleet Intelligence. Although she appearead a bit tired, I found her to be entirely cooperative as she explained her healing technique to me. Essentially, she narrows her focus—her mind and Force-awareness—until it becomes microscopic. While her physical body remains unchanged, her projected form shrinks to an infinitesimal size. In that state, she can rearrange molecules, take them apart, and build new ones bit by bit.