If Mod B has compatibility patches for Mod A, especially where the compatibility patch is a replacer, you may find that uninstalling Mod A leaves what appear to be Mod A files behind. Here's an example from Fallout 4. I install the Better Settlers mod. I then install the Unique NPC's mod. Unique NPC's has compatibility patches for Better Settlers, including a replacer for the BetterSettlers.esp file, as they redid the face geometry to match their own. Uninstalling Better settlers leaves several files behind, including BetterSettlers.esp, as it came from a different mod. And I'll never know it if I don't look in the Data folder as Vortex has added a layer of abstraction that hides it. So you may need to identify and reinstall every other mod that has compatibility patches for the mod you are trying to remove. That's no real problem with a small number of mods, but becomes an issue when you have several hundred. Vortex is supposed to be a mod manager, but it is failing to effectively manage mods in this instance. It should know when it overwrites a file from another mod.