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Oh, okay! Thanks for letting me know. Now I don't feel so frustrated thinking that I missed something, lol. For the other routes, (both Jon and Katy's) will I still get the good endings for the characters if the relationship is in 'soulmate' but there's still a little left unfilled?

Yes, you can still get the good ending as long as you've seen their last romantic event (Usually a confession) and you've maxed a certain stat. Example, you will unlock Liz's good ending by making your deception at least 120 (Deceiving). You can see here for more info https://gameplay.tips/guides/1071-amplitude.html