How much do i ask for back?

I agree 50%. In the end they might be able to edit the video to make it less awkward that they lost audio but it is still a huge issue to be missing that part of the ceremony.

I would think asking for half is fair. You seem to have a kindness about you and an understanding of the situation, as long as this comes across to them in your correspondence I think you're good. Try to do this mostly over email so it's all documented.
Hi X,
I have been researching a little and trying to think of a fair price, it is hard to figure out exactly what to do in this situation! The video is wonderful, thank you for doing such an amazing job on it. Unfortunately, my husbands speech to me was very important, and honestly one of the only reasons I really wanted the wedding to be captured on video, to not have it is upsetting for us and our family and friends who were unable to attend. Do you think 50% would be fair? When looking up what others have done in this situation and asking around, this is the number I seem to be finding, as video is half of the job and audio is the other. Let me know your thoughts, I'd love to discuss if you think fixing or rerecording the audio is worth it, if the final product turns out alright, we could discuss cutting 30% or more if it's fantastic. I know you are more knowledgeable as to if the end result would be worth it.

Thank you so much again for your how professionally you have been handling this situation.

I would for sure ask for at least 50% back. What kind of videographer doesn't bring a backup mic in case of an emergency? That's his job. He couldn't have called someone to bring a backup? Or ANYTHING other than resigning himself to creating and delivering a subpar product?

I wouldn't be rude about it, just matter of fact. And I certainly wouldn't undercut my initial offer in the same email or act like they're doing you a favor by giving you a discount (i.e. say you're fine with only 30% off if they don't think 50% is fair?? Huh??). The whole point of a wedding is the exchanging of vows. He didn't capture that. Period. He needs to refund you what he failed—half of a complete video (audio + imagery).

It doesn't matter that he/the owner only charges $1,000 for three hours of work + editing. He/the owner set his prices, not you. The dollar amount doesn't matter, the percentage of what he failed to deliver does, which is 50%.

Yes, this makes sense. For a service such as photography/videography, the service goes beyond the 3 hours on site because editing can take several hours.

She sounds great, if I was splurging for a videographer I'd totally ask for the name and number! Very professional of her.

I'm so glad you got this resolution! I told my DH about this last night after I commented and he said he would have asked for a full refund, and hearing his reasons, I totally agreed. I'm glad the business owner agreed and it sounds like she's professional enough to improve her business moving forward (i.e. have backup equipment!).