I don't use Ortus but what's probably happening is that that the Ortus STVI is still enabled and is still getting imported every time you start Sage, effectively undoing your changes.
So the first thing you need to do before you change anything is to decide what sort of component you're trying to add to the plugin ecosystem. Are you trying to make a new STVI that replaces the Ortus STVI? A mod that loads on top of the Ortus STVI? A whole new STV that has everything preloaded and doesn't require any STVIs? Your answer to this will determine how you do your Studio editing and how you save the results.
Let's assume that you want the second option, i.e. you want to continue to use the Ortus plugin, but you want to make a small plugin of your own that modifies its effects (as opposed to cloning the Ortus plugin and maintaining a variant copy of it yourself).
In that case you're going to start with the base STV and the Ortus plugin enabled, and disable all other plugins. You're then going to save a copy of that (using the Save A Copy As command,
not the Save As command) as a snapshot of where you started.
Then do your edits, moving menu items around or whatever.
Then, instead of saving the result as an STV (remember you're not trying to make a whole new STV here, you're trying to make a small UI mod), you do a UID File Difference against the snapshot you set aside earlier. This will show you exactly what changes you made, and only those changes (and if it shows you more than that, then you did something wrong somewhere). You can then use the Generate STVI button to save just your changes (and nobody else's) in STVI form.
Then you need to package up that STVI as a UI Mod plugin, with a dependency on the Ortus plugin you're modifying. (Information on how to package plugins is found in the
plugin developer's guide.) Then reload the base STV and use the plugin manager to install your UI mod.
After you've done all that, your mod will be loaded automatically on startup, after the Ortus plugin has been loaded. It's because UI mods are loaded dynamically on startup that you must go through all these steps to abstract your edits in a form that can be reapplied automatically, and register them with the plugin manager (with appropriate dependencies) so it knows when to reapply them. Just saving a snapshot of an edited STV doesn't do any of that.