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Something that tripped me up for a bit after updating my flake was the new cacheDir.
This new cacheDir is currently defined as default = "/tmp/agenix-rekey.\"$UID\"";.
This creates new directories for each user running rekey (as far as I understand). However, if you don't add the users explicitly to trusted-users and simply follow the readme and add nix.settings.extra-sandbox-paths = ["/tmp/agenix-rekey"]; to the configuration, rekeying will always fail.
My suggestion would be to change the default cacheDir to default = "/tmp/agenix-rekey/\"$UID\"";. This would create the uid-directories under the agenix-rekey cacheDir and make setting the extra-sandbox-paths easier.