Except that for some people, you only have a SHA1 hash, and for others, you only have an scrypt hash. Since they (I hope) weren't storing the plaintext (pre-hash) passwords alongside the hashed versions, the only time they can change the initial hashing mechanism is when passwords are provided to them during a password change or user login.
Hash all the sha1 passwords with scrypt. Hash all new passwords with sha1 then scrypt.