Ah yeah, been there, and probably the first time was when renaming a function but missing to update callers, so callers keep calling the old function, and you have no idea why the changes you made in the new function aren't working.

I have a this little function for clearing the current namespace that I call every time I rename any var inside a namespace:

  (defn clear-ns []
    (map #(ns-unmap *ns* %) (keys (ns-interns *ns*))))

Not a perfect solution, but personally I also don't know a better solution that doesn't involve loosing out on other (non-negotiable for me) benefits.