Consolidating Badges

My organization has a similar model. We have a set of five courses, three of which cover a skill set (the other two are an Introduction and a Closure to the overall program). We bundled all five into a learning plan, and there will be a facilitator who will interact with the learner audience and recommend specific courses based on need. We're awarding a badge for each course completed, and a sixth badge for the completion of all courses within the learning plan. 

We asked one of our graphic designers to create a set of badge icons, with a distinction (in pattern and design) between the course badges and the learning plan badge. When viewing their badges, learners will be able to see both from the badge titles and the icons themselves whether they have an individual course badge, or the badge representing total completion of the program.

The result is that learners who have completed all five courses will still have all of the badges in their record (so, as @Bfarkas mentioned, there's no automated swapping out of the piece-parts for a whole), but they'll be able to track and identify their progress.