If you can only erase bits 100 at a time, you don’t really have 100 bits, do you?
Now we set things up so that the bit strings that aren’t all zeros have an energy of and the all-zeros bit string has an energy of 0.
Now your thermal state just equalizes probabilities across those nonzero bit strings.
Drexler’s calculations concern the thermal excitation of vibrations in logic rods, not the thermal excitation of their translational motion. Plugging his own numbers for dissipation into the fluctuation-dissipation relation, a typical thermal displacement of a rod during a cycle is going to be on the order of the 0.7nm error threshold for his proposed design in Nanosystems.
That dissipation is already at the limit (from Akhiezer damping) of what defect-free bulk diamond could theoretically achieve at the proposed frequency of operation even if somehow all thermoelastic damping, friction, and acoustic radiation could be engineered away. An assembly of non-bonded rods sliding against and colliding with one another ought to have something like 3 orders of magnitude worse noise and dissipation from fundamental processes alone, irrespective of clever engineering, as a lower bound. Assemblies like this in general, not just the nanomechanical computer, aren’t going to operate with nanometer precision at room temperature.