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Yes, this is secure, even though scrypt uses PBKDF2 inside. PBKDF2 has the issue that it the work factor is required $n$ times where $n$ is the number hash outputs concatenated to create the final PBKDF2 output. That means that if you can check the validity of PBKDF2 using only the initial bits (in your case used for the key if the hash was SHA-256, for ...

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