I'd say it's best if the story prevails, cutting a bit of romance but keeping the separate routes still allows each character to have a customized storyline which feels very satisfying in the multiple route format and encourages readers to explore each one for the full story. It's just good! Shared scenes are usually the go to for these sorta things as well but given we're already locked in with one third for two routes and halfway for the other, I don't think wasting time on rewrites is a great idea