I would use "acting CEO", or in a very formal or serious situation (grave illness, maybe): "CEO pro tem" (short for pro tempore, i.e. for the time being).
If you're looking for a word which can describe the person's role (not title) as a backup to the boss, whether or not the boss is currently absent, then I suggest exactly that: either backup or understudy. As in "Bob's my backup in case I have to leave early" or "Umberto is understudying me [or is my understudy]"