Typically, having asked the question, I find an answer for myself.

In this case, I created a brand new stencil and copied the legend shape on to it. From VISIO's perspective, the legend shape has no memory of its previous incarnation. I can create a new improved version of the stencil shape and log it into the Legend, with out getting an unwanted version number like "Limestone 13".

The essential requirement seems to be that the user must employ a new stencil.