We bond our bunnies because we want them to have a friend so they aren't lonely. But the problem that can be encountered with that is that when it is a pretty new bun, that it doesn't give us the time needed to bond ourselves with that individual rabbit, because they are busy with their bunny buddy now. I just think that you and Clem haven't spent enough individual time for her to feel completely comfortable with you and form that needed bond, and that maybe her behavior has rubbed off on Felix. It may help if you spend some one on one time with each of them in a separate room from their buddy, preferably a small room like a bathroom, so that the bun isn't spending a lot of time wandering off and exploring, but is actually right around you the whole time, getting to know you better and feel more comfortable. You can provide activities and fun things for the bun to do, and feed treats and veggies. You just want to make it all positive, so that they associate the experience with good things.
If you are concerned about separating them affecting their bond, or if they show signs it is, then you can try doing it with both buns together. You just want to make sure to do it in a small area so they are right around you and a lot of the focus is being around you.