Hello.
I have a quick suggestion/observation regarding a thing I commonly have to do in Zbrsh.
Some operations (such as Surface>Noise) and their settings are stored within the Zproject save file. Sometimes this information conflicts with other z plugs such as transpose.
For example add noise to a mesh, bake noise to surface (but noise info is still stored) and if you were to then go down in sublevels and use transpose master without hitting DELETE noise under surface menu (even though already applied to mesh) , subtool master would not work.
Now its not a big deal, you can export the subtools you need to transpose as a ztool, import to a clean project, pose and reimport back but sometimes using many subtols its a bit time consuming .
How about a delete history/clean up project settings button ? Alot like maya delete history kind of button that cleans node settings ?
Though might be worth sharing it might help someone 
Vick.