With the update window, in general, things aren't automatically saved. However, due to what seems to be buggy or quirky behaviour by Grasshopper, these "parent" nested clusters aren't marked as modified, and even if programmatically set as modifed by the DefinitionLibrary plug-in code, Grasshopper doesn't prompt users to save these clusters to file.
As a result, for now, the DefinitionLibrary plug-in explicitly saves all file-referenced nested clusters that are the "parents" of the cluster being changed.
With the update window, in general, things aren't automatically saved. However, due to what seems to be buggy or quirky behaviour by Grasshopper, these "parent" nested clusters aren't marked as modified, and even if programmatically set as modifed by the DefinitionLibrary plug-in code, Grasshopper doesn't prompt users to save these clusters to file.
As a result, for now, the DefinitionLibrary plug-in explicitly saves all file-referenced nested clusters that are the "parents" of the cluster being changed.