To be clear the physics behavior issue and chipmunk behavior issue are two independent issues.
I can only speak for the chipmunk behavior though.
A save/load will do nothing for the chipmunk behavior, and in fact I didn't make saving/loading do anything.
The only way to "refresh" is to reload the webpage.
I probably won't have time to track down where the leak is in the behavior.
In the meantime a practical solution is to maybe diminish the amount of leaking so it can run longer.
Creating less physics objects is an obvious thing to do, but it's probably not the issue here.
Less obvious is every time a physics object changes size, or changes animation frame, or in the case of the tilemap is modified then that actually causes stuff to be recreated in the physics engine.
So if you want an animated Sprite to have physics then instead pin the animated Sprite to another Sprite with physics.