This actually looks like a series of problems which are related but have slightly different answers:

My question is how do I make potential updates to some of the content and ask colleagues to go in and complete the new content without them having to retake the full program?

Updating isn't difficult (just make the changes to the existing course), but getting colleagues to complete the new content is tricky. In theory you could reset the completion records for the course and get people to complete it again, but that doesn't feel like a very elegant solution since it will get rid of their existing data for that course (but not the whole program).

So they will need to complete all the of the program and complete the new/up to date content and not the old content? How will they know which version is the up to date content they need to complete?

If you just make changes to the existing course, then they will always just be doing the up to date version.

Will we need to create a new program every time there is an update (we will limit this to once per year) and then upload the historic course completion data, which will then show only the New/Update content they will have to complete?

That's certainly one solution, but I'm not convinced that it's the best. I might be tempted to update the content in the existing program (so that new starters get the current content) and then create a dynamic audience with the criteria "Completed Program X before" and then set the date you made the changes. You now have a set of people who need to complete this updated course, but the question is then how you will push the learning out to them. You might well find that you need to duplicate the updated course and push it out to that audience in a new program, because I'm not sure a certification is quite going to do what you need, but certifications are certainly worth looking at if there is a refresh cycle for learning.

Dan