I get that bonus missions are intended to be side objectives that you don't have to complete for every quest, but I would really like it if they wouldn't get removed my mission log when I finish the main bits of a mission. This is especially annoying when I'm doing a bonus mission series (ie. multiple stages) and while on the last stage the bonus mission magically goes away.
My suggestion is to uncouple the bonus missions from the main mission. Just give me both missions at the same time so that I can finish them both without having to worry about loosing EXP and Credits.