I wasn't gifted with the ability to write grand imposing essays, do instead I'll keep it brief.

Could the key to skill & purpose deterioration in an ark ship simply be a techno primitivist approach to things?

Instead of having a couple machines make all the things, how about going as primitivist as possible and having as much know-how rest within the crew, all taught by sub-sapient machines?

Instead of, say, having shoe factories we're instead offering shoemaker courses.

Instead of cranking out repair robots we're Training a fleet of mechanics to analyze and repair equipment with nothing but pen, paper and some unpowered tools.

Etc.

Keep things resilient by giving everyone something to do and making the crew itself part of the redundancies.