Only problem is of course the sudden potential energy change.
That is, two bots overlapping all of the sudden can cause a case of energy from nowhere. Like one electron suddenly creating another, both overlapping, both with a great deal of (perhaps nearly infiinite) potential energy.
That shouldn't happen with the physics that I set up a few releases back. There is no longer any repulsion field so no accelerations are ever applied to overlapping bots.
All it should do is physically displace both bots away from the combined centre at a rate of half of the physical overlap per cycle. No accelerations! just a gentle push that decreases displacement as overlap decreases.
You haven't changed the physics have you?
If not then I repeat, just calculate the amount of overlap and from this work out the combined volume. Then just apply a corrected diameter to each bot as they slowly separate. It should take about 10 cycles for them to part ways. Just give them a very small offset of a couple of twips to set them on their way.