There are three types of Karma:
1. Sañcita (stored karma)
2. Āgāmi (future karma)
3. Prārabdha (started karma -which is already active-)
The passive saṁskāra-s (impressions manufactured by past actions) are stored in the causal body in deep sleep because they are not actively occupied in creating pleasure and pain during the present lifetime. These kinds of karma are known as sañcita and āgāmi (stored and future).
On the other hand, the type of karma which is actively busy with granting the good and bad fruits during the current lifetime is called prārabdha (begun). It has started with this lifetime and will not be over till the body dies. As it is giving pleasure and pain, it is working at the level of the subtle body (and not at the level of the causal body as the previous two kinds of karma).
During Liberation, if you are to retain your physical body, then sañcita and āgāmi are destroyed but prārabdha stays. Why? Because without the fuel of karma there is no life in a physical body.
In the case of the videhamukta-s (the ones who abandon the body during Liberation), all the three types of karma are destroyed, but in the case of the jīvanmukta-s (the ones who retain the body during Liberation), only the first two types of karma are annihilated.
Besides, as regards the question about why not leaving sañcita or āgāmi active instead of prārabdha, the answer is simple: Because the prārabdha already began and manufactured the physical body in order for it to experience the consequences of previous actions. If another type of karma could be left active instead of prārabdha after Liberation, so the form of the body would have to drastically change as the entire set of new saṁskāra-s getting enabled demand another kind of body for it experience the respective fruits. A dramatic change in the form of the body of the Great Yogī would be disturbing to everybody around. As in general, the Great Yogī will tend to keep his achievement of Liberation hidden, this disturbance regarding the drastic bodily change is not welcome. OK, enough of revealing this!