We used to have a deaf aussie/bc mix that would do the same thing. She'd twitch her feet and whine sometimes. I didn't mind her twitching her feet but when she started barking or whining I woke her up and she was fine.

Maybe talk to your vet about it? I also agree with what Cincy'sMom said - if touching her gently doesn't stop her twitching, that could mean there's a problem. Maybe it's just another phase? Like you said, she went through it when she was a puppy. Maybe she'll stop again.