It's not cool for 200 commits to disappear from master. Given the goals of this project you should probably be trying to signal the presence of qualities like robustness, reproducibility, reliable audit trail. Treating the git repo like its a local scratch filesystem is at the opposite extreme. I see they're in another branch, but that's not the point.
When you want to switch wholesale to another set of sources, do it like this:
git merge -s ours origin/mark-i
It has the same effect in terms of the work tree, but doesn't stomp on the history. (You can still do this in master.)