There can still be fleas that you just don't see, but yes the flea allergy from bites can last a few days... if the itching is still really bad (ie scratching/chewing themselves raw) then maybe consider a vet visit for an injection to help with immediate relief. Remember: all current fleas on your pet may be gone, but they may be being exposed to, reinfested and/or bit by new fleas from the environment trying to hitch a ride so even if they aren't physically on your pet anymore, they may be hopping on, biting, and dying... which causes itching to start all over again.

The pupae can lie dormant for MONTHS before hatching. It's a survivability tactic if conditions aren't favorable for hatching. That's why its important to keep your pets on a preventative for a few months consecutively as well as adamantly cleaning your household for a few months. The advantage works throughout the month; it isn't like a dewormer that gets rid of all current pests and then you get reinfested as the month goes on. If a new flea jumps on them at the end of the month, the product should still work to kill them. Granted, the percentage of effectiveness starts to decline the closer you get to the end of the month and I dont know what it is specifically with Advantage but it should still, theoretically, work.