You can always generate a whole new system for the NPR- then you won't know where it links to (think dormant links.) Anyway, when you generate the NPR, their fleet and tech will be pre-built. I did this in my current game, and shortly after first contact, noted they had a lot of ships... and with some espionage, discovered they had anti-matter core engines(!) (Two tech levels above me, at least. Luckily they were friendly, as shortly after, the Invaders appeared.)
Anyway, be sure you give them enough RP that their tech will make them a challenge. No fun invading a planet where the indigenous population's throwing rocks back at your power armor.