Lucifer is a ludicrously resource/cost high technology for application
Lucifer is a discontinued line stranded in the local subspace region
Lucifer was deployed as a scaled response to the local situation which did not anticipate an alliance between the local species
Shivans are no longer able to create more Lucifer destroyers for whatever reason
The Shivans in FS1 and FS2 are not actually the same group.
Lucifer is not deployed against civilizations that have demonstrated the capacity to destroy it.
Lucifer is expeditionary, Shivan fleet in FS2 is not.
Lucifer isn't expeditionary, Shivan fleet in FS2 is.
Lucifer fleet is newer or older than Shivan fleet in FS2 and reflects different doctrine or technology base.
Lucifer is considered flawed design after its destruction prevented the Shivans from completing their attempts to destroy Earth. (Something they apparently had a shot at doing, c.f. Hellfire in Silent Threat.)