From the reference manual's description of the Prototype Interface,
when a definition is updated, thename,pos,show,locked,animated,volatile,font,pattern, andscriptattributes of Contraptions will be preserved, as well thevalue,scroll,row,col, and image content of the widgets they contain (as applicable) if they have been modified from their original values in the prototype, but everything else will be regenerated from the definition. The state of contraptions is kept, and the behavior and appearance is changed.
Any other state that you wish to survive prototype modification should be stashed in internal widgets; I recommend refreshing these settings (alongside applying settings from the enclosing contraption instance like .font and .locked, where appropriate) in the view[] event handler in the prototype script.