Unfortunately, we are entrenched in an age of education that wants to be "pretty." Students are all reaching "mastery" in every subject and they all move at the same pace through every class every year. Like all utopian societies, this is not attainable. True learning is ugly (to outsiders), and we need to embrace that thought before we can move forward in education.
When I am asked about what things should be done to flip a class successfully, I always respond with good pedagogy, collaboration, and reflection. If we are not reflecting, we are not growing. If we are reflecting properly, student voice will also be a major player in decisions as classes move forward.
I like to think of class adaptations like I think about Facebook changes. The outward appearance changes and people lose their minds about how terrible the new design is and how they want to go back to the old, familiar way of doing things (status quo). Teaching is no different. When a teacher flips for the first time, students are put under the microscope and they hate it...at least in my experience. They have to unlearn how they have been
learning playing school up until your class. Needless to say, student surveys usually do not go well the first time they are asked about the new style.
Second, grades are imperfect. Students that play the school game well get good grades...that is just the way it is. Learning is messy. It requires failure, and in today's grading atmosphere, that usually means a lower class average. Do not define your teaching by the grades of your students. Talk to other people (parents, students, administrators, colleagues) about why true learning is so ugly in the grade book...it is not rewarded by the traditional school model. Do not sacrifice what you know is right for your students because of a number on paper.
I want to encourage you, if you are flipping for the first time, to look at your survey results as reflex reactions to a new environment, and not necessarily as a success or failure in your book. You will never have 100% satisfaction or love from students, so do not expect it. If it is your first time, I would expect your results to be split 50-50. The first few weeks will be hard, and we do not talk about that enough. But, take heart...it does get better.
Listen to your students and work with them. Find ways to compromise on expectations or methods. Take their advice on how to improve instruction. Reward failure and look at the big picture being painted. Watching students learn is beautiful, and we need to begin to recognize the process, not snapshot performances. You, the teacher, know what is best for their learning, so keep doing what is right.