Thank you, thank you, thank you, thank you, thank you............
The first person to ever acknowledge the folly of the CC populating the past encounters. I like your method. I do, as stated, something similar, which is to leave it blank and put the CC in the top line of the HPI. It's kind of funny. Even though CC is on the progress note, it is kind of cool that the final diagnosis is there in bold letters.
A little like the consultants who start with Assessment and Plan and then do the Subjective and Objective.