Because they have far more than military aircraft interests here in the UK. They are a vast outfit and are still acquiring niche UK manufacturing companies in the defence and security market. Detica being a notable recent one.
They have over 30 manufacturing plants in the UK, there is a LOT more to BAES than merely Warton and Samlesbury. Samlesbury will be designing, engineering and manufacturing F-35 airframe assemblies for a very long time.
Mantis and the like will keep Warton busy too. Plus Typhoon will be upgraded a few more times and they are also still active in the export market. In the REALLY long term future, while everyone talks of the F-35 and Typhoon as being the last generation of manned combat aircraft, I recall when that was said about a certain English Electric Lightning...
It's not all doom and gloom in the world's second largest aerospace industry you know!