In a token bucket algorithm you don't actually have a separate replenish step, it is baked into the next check you do. Similar to how in the example you linked the removal of the old entries is baked into the check step.

Check out my example: https://gist.github.com/ptarjan/e38f45f2dfe601419ca3af937fff... on line 23 with

    local filled_tokens = math.min(capacity, last_tokens+(delta*rate))

that adds in any tokens that should drip into the bucket since the last check.