If you happen to use some Linux distro you should be able to use XDG_CONFIG_HOME environment variable and start kicad from scratch. The upcoming version 5 recognizes that and KICAD_CONFIG_HOME on all platforms, but v4 unfortunately doesn’t, so this option is limited to *nix systems. Then, if the global fp-lib-table is not what you want you can change it without affecting other projects which you start with the old configuration. See Any ultimate Guide on how to use KiCad 4 and 5 on one System? and the document I link from there for details about using environment variables.
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