Currently system metadata consist of three "levels":
QuadStorages? contains only "symlinks" to maps, if you drop a storage you don't drop all mappings inside. If you drop the DefaultQuadStorage? or some other built-in thing, it can be safely recovered by DB.DBA.RDF_AUDIT_METADATA, with first parameter set to 1. This will keep your own data intact. However we recommend to write a script that declares all your formats, Linked Data Views and storages, to be able to reproduce the configuration after any failures.