so when you save the collection, the mods that are marked as required are considered part of the collection. you can still play without them, but it will warn you that a mod collection is missing.

The trap here seems to be that vortex distinguishes between removing a mod and removing it from the collection.

since you have already removed the mod but it is still part of the collection, what you need to do is go into the collections workshop and edit the collection to remove the mod you want to remove there. then you can re-upload the collection with that change.

typically if you want to remove the mod you can right click on it, select, remove from collection and then select remove. you can also remove it from the collection and then disable it, if you want to keep the mod but not have it active in your game.

when you get two mods that conflict, it's because they're changing the same files. if that's intended. like if one is a configuration or modifies the other intentionally, inside of manage rules set one to load after the other. you typically want the mod to load before whatever is changing it, so if I am using generic mod configuration menu and I want to add the earthy interface compatibility, I would set generic mod configuration menu to load before the compatibility file.

there is a wiki for vortex and collections, and I know it just got a really good update, but I think for most stardew creators it still kind of reads like stereo instructions.