Currently when a civ declines it almost never recovers ie few planets = poor tech, poor econ etc. How about:
When a civilisation is on the verge of being wiped out or sverely declining there could be a possible event that overthrows the current leader and creates an evil dictatorship. The dictator would have a number of special military and economic powers such as forced labour, suicide ships etc that would make the last few planets much harder to wipe out. If the civilisation recovers then the original leader who had managed to escape into exile might be reelected.
Roq