Well it really depends on which character you are using. Every character has a different way of dealing with flowcharts (for this example, Ken).
When you know they are gonna jump in with j. HK>cr.HK, AA them before they hit you with either HK Jag Knee with Adon, MP SRK with Akuma, b.st.MP with Adon, or st.HK with Bison (while they are a bit further away with him). These are their best options.
If it's already after he did cr.HK, there's not too much you can do. Even though cr.HK is -7 on block, it pushes him far from your faster normals to attack. Though you can still attempt with a counter sweep with Adon or Akuma.
If they keep jumping back, don't fall into the habit of jumping after them. Just slowly walk forward and block their fireballs. If you're Akuma, just throw fireballs back. It's really just practicing in training how to punish. That's really the best option of knowing what to do.