Hmm, after copying over the instancesCount then it works:
clone._thinInstanceDataStorage.instancesCount = source._thinInstanceDataStorage.instancesCount;
For example here’s your PG with this fix and also here’s a simpler PG to show the issue (if you comment out line 45 then you can see how it isn’t working without setting the instancesCount).
EDIT: I started a new thread for this issue of needing to set the internal count directly since it turned out to be unrelated.