This sounds very, very interesting. I would definately want in on it. Oh, wait. Assuming I have the time, of coarse!
As to the ship tech question, In my opinion, the ships you currently have built would work, but any you have in your build queue would be lost, and you wouldn't be able to build more until the tech barometer rose above Battlecruiser again.
On second thought, that might be hard to implement. The only way I can see this working would be to have the techtree data file (or whatever it's called) changed along with the components.txt. (And the facilities.txt? Suddenly your research centers go from cranking out 913 research points to 100? Ouch! Shipyards construction rate crashes? Bigger ouch!!) But does anyone know what would happen when the tech tree changes and a tech you have researched no longer exists? Will the research level stay, but you can't use it's components/facilities; or will you have to research that tech level all over again when it comes back? Having to re-research would _SUCK_!