So I'm trying to edit one of my beatmaps that is for all modes in Edit mode. How do I change a part in it in osu!mania mode without it asking if I want to remove all the notes and start over? 
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You can't, if you really want to edit your beatmap for mania, you have to create a new one. Implicitly, "all modes" means "osu!std" and the map is automatically converted for each other modes