We can't explain chi with science because chi doesn't exist.
And, yes, being able to explain things does make them less magical.Not magical in the sense of wonder and awe, but by definition magic implies something that is unknown and unknowable. Look up the literal definitions of the words 'occult' and 'arcane'. Also look up Clarke's law.
Magic implies something apart from science which cannot be explained, at least not entirely. Many people have enough trouble understanding science as it is without people comparing it to magic.