To clarify publicly, each run of a bot is treated is a new instance, which is consistent with most SaaS (Software as a Service). We offer a grace period in which within the first hour of a bot execution you can stop and restart and not be charged again because it will re-attach you to the old instance. Beyond that grace period it will create a brand new instance. The best solution for changing settings during runtime is to encourage the Bot Author to allow that in the code. In fact we may start enforcing premium Bot Authors to do that, but for now ask kindly.
Sidenote: The Staff members do not and cannot read all of the thousands of posts made across all the threads in all the forums on RuneMate. We keep a close eye on certain forums like Client Support, because they are the most important. If you need our attention there are many ways to reach us, including PM, profile posts, and creating threads in the appropriate sections. For most situations the last option is the most appropriate.