The Vilani tech base was extremely mature, stable, and resistant to innovation - but that wasn't because they were incapable of it. Everything that they had now, they'd originally invented for themselves at one time in the past. Quod erat demonstratum, the Vilani gene pool was potentially capable of producing creative geniuses. Even if they were apparently much rarer there than here - and that was still just me guessing - they still existed, and I was living proof that if the discovery were groundbreaking enough then you only needed one genius to change things. And there were trillions of Vilani to help improve those odds. And reverse-engineering was substantially easier than discovery.
I'm rather unaware of the setting, but I have to assume the reason why the Vilani don't seem to have a constant stream of geniuses is because they have a caste system. Their accessible pool of geniuses is only as big as their scientist caste. Then you have to shrink said pool down further; how many members of the scientist caste are sidelined or ignored because politically there are more important, more
noble scientist caste members. Ones who are older or have greater power, the ones who decide which projects are worked on or even get present to the ruling castes for funding. Then you need to cut that pool
even further for every potential scientist caste member from a powerful scientist caste family who also manages to innovate or invent even when surrounded by a culture that more highly values refinement and reliability.
Sophia might not of thought of it yet but the Vilani's pool of geniuses is extremely small. Likely smaller then Earth's honestly.
So I didn't just have to invent something wondrous enough to break the stalemate. I had to invent something wondrous enough to break the stalemate and that the Vilani could not reverse-engineer to regain the advantage.
I guess there are four possible solutions to this;
Using a techbase that is hard to reverse engineer. Because it was designed to be hard to reverse engineer (like Battletech, where the Star League put a lot of effort into making their stuff really hard to figure out). It uses a techbase that is so foreign to the Vilani's knowledge base that before attempting to reverse engineer it the Vilani have to spend at least a generation or two trying to understand how the hell its even possible. Something that uses eldritch physics or functions in such a way it might as well be magic. Or because its something that the Vilani are just traditionally weak at studying, like biotech. An example might by Tyranid weapons.
Using technology that has a resource choke point the Vilani can't overcome. I don't know if Sophia can learn how to create resources, but if she were to figure out how to produce, say, element zero that would provide a good way to avoid the Vilani from reverse engineering any Confederation weapons. Make sure any (insert resource here) production facilities are protected religiously and it doesn't matter how many weapons factories they infiltrate or pieces of gear the Vilani capture, they won't be able to replicate it.
Using technology the Vilani can't or won't take advantage of. Something that might work really well for a small army but is useless for a larger one, though no example comes to mind. As for technology the Vilani would refuse to take advantage of? The one that does come to mind is FTL communications. The Vilani are a feudal empire, with noble houses controlling various worlds and the highest noble houses controlling the imperial throne. It is a very de-centralize power and the various noble houses probably like it that way. FTL communications brings with it the potential for centralization. Many nobles will realize that the wide spread use of FTL communications will mean the shrinking of their authority as the emperor is only a single phone call away. It means the highest noble houses will get to have a constant say in how the other nobles run things. I would fully expect most noble houses to resist the introduction of FTL communications because of how much of a danger they are to their power.
The final option would be to just go full mad scientist and only build super weapons. Go crazy and build something like the star wars 'Executor' that 19 km long flying city with the miniature deathstar gun that one shots ships. Load it up with shields and turbo blasters and, this is the most important part,
only build one of them. If Sophia wants to avoid the dangers of reverse engineering, one of the best ways would be to avoid mass production. So in that case just build superweapons, because if the Vilani manage to bring those superweapons down then the Confederation is screwed anyway.