I don’t know about the mission breaking or anything like that.
But you can remove quests through the debug menu. It does warn that this is an unstable debug option, so I don’t know how it might negatively affect you. So, I don’t know, maybe you shouldn’t do that? But it’s an option.
Open the menu and press ‘d’ to edit self/npc, then select yourself, then press ‘M’ to edit missions, then select the mission you’re talking about, then do whichever option you’re looking for.