I think it will depend on what the patch entails. If it's new content that has been added then it shouldn't matter too much. I think the missing stuff should be taken care of by the default data in the compiled vis file.
Also exporting everything as individual packages as opposed to compiling everything to the main vis file should reduce the risk of causing bugs due to outdated save files.
Something that could potentially cause an issue is if you edited / removed / renamed existing conditions / values / characters / scenes, etc. as the xml data would be trying to read & apply changes to something that no longer exists. For example, if you were to delete a scene & then remake it, then everything from the scene itself, to everything you added to the scene would have new ID values, which means that all the saved data (in an existing save file) related to that scene would no longer be valid, so the engine may resort to default values set in the vis file, even though the person playing the game may have already done everything in that scene. What I've just said is a theoretical example, but it is something that could potentially happen.