"After a client had performed Step 1 but HAD not performed Step 2, he/she will.."
OR
"After a client had performed Step 1 but HAS not performed Step 2, he/she will.."
I think the first one is correct because he/she WILL .. AFTER both HADS. Yet, another part of me thinks the second one is right, because "HAS not" is stating that the fact happened before now.
Your first sentence is nearly OK, but the will doesn't fit. The second sentence is odd.
When we use the present perfect ("has performed"), we are choosing to relate some event in the past to the present. The nature of that relationship can vary: it might be something very recent, something that has continued to the present, something that took place a while ago but we are choosing to see as embedded in a period that extends to the present, or something that is complete but has effects in the present.
When we use the so-called past perfect ("had performed"), we are choosing to view some event from a later point in the past.
In your first example, the two had performed are consistent with each other, and imply that you are choosing to look at the client's actions from some later point in the past; but the non-past nature of will is then inconsistent. Change it to would, and the sentence is fine.
In your second example, you first start with a perspective in the past, but then the has performed is relative to the present. This unexplained shift is disorienting for a reader.
