There is a certain bug that prevents highlights and annotations to be visually marked on the screen. Those highlights and annotations are however listed in the annotation list. This bug concernes (mainly?) kepubs. If this is what your are experiencing, you can find some information
here, and there is also a link with a suggestion on how to make those highlights/annotations visible.
This tool (for Windows) has also a function to do this. There is however a drawback to this (cf. the documentation). This drawback is the same whether you use the tool or do it manually.