In thaikick's original post, he specifically states that the custom templates he coded from scratch (but didn't move from the plugin's folder into his theme folder) were lost, so I doubt he was referring to the settings which get stored in the database.
In your case, unfortunately I don't have an upgrade process in place when moving between MAJOR versions of the plugin. If you're already running version 3.0 or above, then going to 3.0.2 won't cause any issues.
And, even when moving between version 1.x.x or version 2.x.x and version 3.x.x not all settings will be lost. It really depends on what you've configured for each widget. I use the plugin on about a half dozen live sites, some of them with multiple instances of the widget. Even with the ~12+ widgets out there, it didn't take me long to reset the post types & tax/terms selected for each widget. These are the only settings that should cause issues. Any titles, ordering, counts, thumbnails & custom template settings should remain intact.
I'm sorry there isn't an easier/better way. Hopefully the plugin has matured enough where I will no longer need to make code changes that will cause upgrade issues at all. That's one of the goals from v3.
Sorry for the trouble,