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Nix has previously replaced index addressing for nix profile installed packages with name addressing: NixOS/nix#9656.
Kup currently uses indices to remove packages prior to installing a new version to replace it (updating packages). This fails, when the respective nix manifest does not support indices anymore. This seems to be case since recently for some users of newer versions, though it does not seem to be entirely dependent on the version of nix in use for some reason. Maybe the manifest has to be upgraded respectively as well.
Kup should switch to using installed package names (typically a combination of the package name and some number) to address packages to be removed. Additionally, the user should be prompted to update nix in case addressing by installed package name is not yet supported with the provided revision of nix.