In Nexus Mod Manager, whenever you install a mod which is editing the same files as another mod, you will be presented with an override prompt upon installation. In most cases your NMM installation will have several file conflicts which you simply are not aware of, whereas Vortex will inform you about the conflicts, and offer the option to resolve them (in different ways) without having to reinstall the mods in question. Nexus Mod Manager and Vortex have different ways of making you aware of file conflicts and enabling you to solve them.
I am getting a lot of mod conflicts with Vortex that were not there in Nexus Mod Manager.
