If you update what? WordPress or the plugin?
Both of these shouldn’t delete the contents of the Post Type, as long as you don’t change the Custom Post Type name.
If you update anything about the Custom Post type — including not updating the Custom Post type name.
As long as you do not update the Custom Post Type unique name all the content in the custom post type should still exists and should not be deleted.
I’m obviously very reluctant to test this, but I’m pretty sure it is what happened. Maybe it could be developed to not delete content even if Custom Post Type unique name is updated.
Content is never being deleted. At least, this is not something I have built in the plugin.
Shortly it works like this. When you create a post for the custom post type ‘books’ it is saved in the database linked to the custom post type ‘books’. When you change the name ‘books’ to ‘magazines’ WordPress will look for content linked to the custom post type ‘magazines’, which will be empty.
In this way it seems that content has been deleted but it has not. It is just that WordPress can’t link the content to your new custom post type.
There is a plugin which let you move content from one post type to another though.
