잘하시네요 just means "you do [it] well" whereas 잘하시는데요 means "but you do it well/just fine".

I think there is a subtle difference between them. Both are basically compliment for doing good job, but they can be interpreted by context. Let's just say i'm English learner. #1. just for compliment Me: She has a dog. Teacher: 잘하시네요. or 잘하시는데요. In this situation, those sentence, 잘하시네요 and 잘하시는데요, can be used for themselves. #2. if I've done well, but I also have mistake. It's not a big deal, though. Me: She have a dog. Teacher: 잘하시는데요. but you can't use have. you should say she has a dog. I tried to do my best, and my teacher didn't want to make me feel bad. so 잘하시는데요 is an indirect way to say with compliment. - I'm not English native speaker. I hope you feel this answer is helpful, even though my explanation is unpolished.