Lawyers are not allowed to make fees non-refundable in CA. This is a blatant violation of the Rules of Professional Conduct. See CRPC 3-700(D)(2). I would write the lawyer a letter advising him/her that unless you get that $1000 back, you will pursue a complaint with the state bar.
I have added the complaint form link at the bottom of this answer.
Best of luck.
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You are both bound by the terms of your agreement. It *sounds* like he was not obligated to perform on your other matter, but perhaps could have done so for client relation's sake. You should consider trying the fee dispute resolution. But if the agreement says there is a $1k non-refundable fee, then you are probably bound by the agreement. I have seen a similar agreement with a $10 fee upheld by the court. In fact in that case, the attorney somehow got $16k, without having done much work at all. I call these "rock star contracts." I do not use them, but many attorneys do. In essence, you are paying for the right to "reserve their services."
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You can probably sue, you can ask for fee arbitration. If he did any work at all, he may be able to justify the $1000 fee, even if someone decides it was not non-refundable.
Take the agreement and any other documents related to that attorney to another attorney for a consultation.