When he changes the shifts around, he always gives a deep bow (by way of apology)
Every time he alters the shifts, he apologises with a deep bow
「シフトで入れ替わる時、彼は頭を深く下げた」= When he changes the shifts around, he always gives a deep bow (by way of apology) / Every time he alters the shifts, he apologises with a deep bow
※「by way of apology」や「apologise」は「謝るために」、「お詫びとして」という意味になります。
「頭を下げる」= bow
「深く」= deep / deeply
「シフトを入れ替わる」= change the shifts around / alter the shifts