Is it possible to encrypt a CNF?
The application you mention is called "proof of useful work" in the literature, see for instance this article.

You can use a fully homomorphic encryption scheme (where the plaintext is the CNF instance) to delegate the computation to an untrusted party without disclosing the input.

This doesn't answer exactly your question, since such scheme doesn't map a CNF into another CNF, but it does work for the intended application.