There is no precedence for the Deputy to be Chair. The positions are legally separate, therefore if the Chair resigns, it creates a vacant that any other member can stand for. The Deputy retains his/her position unless elected Chair.
Any committee must always have a chair, therefore, if the Chair is absent the standing orders may say the Deputy shall Chair in their absence, but a vacancy is not an absence, and therefore it must be either the first item (new meeting) on the agenda or immediately next item (s/he resigns mid-meeting).