There are three types of Karma:
1. Sañcita (stored karma)
2. Āgāmi (future karma)
3. Prārabdha (initiated karma - which is already active-)
Passive saṁskāra-s (impressions created by past actions) are stored in the causal body during deep sleep, because they are not actively involved in creating pleasure and pain during the current life. These types of karma are known as sañcita and āgāmi (stored and future).
On the other hand, the type of karma actively involved in delivering the good and bad fruits during the current life is called prārabdha (initiated). It has started with this life and will not end until the body dies. Since it is providing pleasure and pain, it is working at the subtle body level (and not at the causal body level as the other two previous types of karma).
During Liberation, if you must retain your physical body, then sañcita and āgāmi are destroyed, but prārabdha remains. Why? Because without the fuel of karma, there is no life in a physical body.
In the case of videhamukta-s (those who abandon the body during Liberation), all three types of karma are destroyed, but in the case of jīvanmukta-s (those who retain the body during Liberation), only the first two types of karma are annihilated.
Prārabdha must remain in his case, or there would be no continuity of life. Furthermore, regarding the question about why not leave sañcita or āgāmi active instead of prārabdha, the answer is simple: Because prārabdha has already started and created the physical body to experience the consequences of its previous actions. If another type of karma could remain active instead of prārabdha after Liberation, the form of the body would have to change dramatically, as the entire group of saṁskāra-s that are activated demands another type of body to experience the corresponding fruits. A dramatic change in the body form of the Great Yogi would be disturbing to everyone around. Since generally the Great Yogi tends to keep his achievement of Liberation hidden, this disturbance related to the drastic bodily change is not welcome. Well, enough of revealing this!