I have noticed this and had it questioned on another topic.
I assume you are referring to vstpresets in your post.
I assume you are making things in cubase.
I noticed that when you edit something and save it as a vstpreset, this can differ from the version used in f.e. an older version of a cubase file.
The content is located on different places, and to continue the work on something, you should use the latest version of it.
This looks as intended since this is in line with non-destructive editing, but when you notice this for the first time it can be confusing.
I now use the vstpreset save method on top of the plugin to create my latest versions of something for the moment.
These are consistently the latest version for me, and i can overwrite it. But yes, older versions of something still are present.
Not quite clear for me how the relation is between al these versions, but this is also present in the Halion 6 package, so let’s wait out for some time and we will get an explication.