How to help one cat accept resident cat

We've had two cats separated for a couple of months now and we open the doors for a couple of hours every night. The new cat is so scared of the resident cat that she'll cry, howl, wail, moan, growl, and hiss every time resident cat approaches her (resident cat is a male, and they're both adults). How do we help her not be so scared of him? He's not really aggressive or hostile, but he does seem to want to get to know her. He even talks to her in a soft, high-pitched voice that we've never heard him use before. We've already done all the things we're supposed to do like letting them smell each other's bedding stuff and had Comfort Zone plugged in but nothing seemed to have worked. Oh, and both of them are semi-ferals by the way. Any ideas?

She could be taking the soft, high pitched meow he uses as a warning or threat. Feliway is commonly used to help distract scent aggression and/or fear. Are they both fixed?

You could try putting resident cat in a cat carrier and allowing her to come out alone, this way she may feel safe to approach him.

We won't be able to put resident cat in a carrier because he's semi-feral and although he's lived with us for a year now, we're still trying to win his trust and haven't been able to pet him or the new cat. The only way to get him in a carrier is to chase him down, throw a towel on him, grab him and force him in, which would of course freak him out. We reserve that kind of extreme solution only when we have to take him to the vet.

Yes, they're both fixed.

It's hard to imagine that she'd be threatened by his high-pitched talking voice because it's not a meow at all. It's actually very cute because it's very soft and gentle. It sounds to us like he's wondering why she doesn't like him, but what do I know about what he's really saying!

The fact that you've had them for a few months and still can't pet them makes me think that the problem could persist for quite some time. Are they fighting at all, or is she just being unfriendly?

They haven't fought, but I guess they could have because we never leave them in the same room unsupervised. The new cat did flatten her ears a couple of times but most of the time she doesn't do that. I don't know if she's being unfriendly, I tend to think she's just VERY defensive because the sounds she makes sounds like she's really scared of him. Resident cat has tried swatting at her but missed, but he only did that when she was trying to run from him and he tried to chase her, so it's not like he goes right up to her and starts to swat at her right away. I wonder if he did that because he got tired of being rejected by her over and over.

This is our first time to have more than one cat at a time -- does this mean we're doomed to keep them separated forever or is there hope that she'll be more accepting?

By the way, we only open the doors AFTER they've eaten, so they wouldn't feel threatened about food.