Similar things happened to me like certain components not being visible on the viewport or some options in the details menu being inaccessible after I played with the project files. My case was the result of a corruption, but can it be also what’s going on here? Anyways, does this happen to a specific blueprint? (You said skeletal mesh at first but then mentioned capsule component so I assume the mesh of question is inside a character blueprint) Could you try creating a brand new one and see if you encounter the same issue on that one as well?
Wait did you say C++? That corruption thing I mentioned can also occur if the code doesn’t get compiled properly before the editor opens up. In fact, I just remembered that my similar issue was also due to that reason and not playing with some files myself. If your character blueprint have dependencies on a C++ class, it’s healthier to launch the project from Visual Studio. (Though it’s funny that I don’t encounter that issue on 5.4 contrary to you, while I used to on 5.3 
)