I have to admit, I find the whole thing confusing. It's basically NexusMods attempt at creating the ability to make mod packs like CurseForge ones for Minecraft, which break entirely if a mod is deleted outright. They definitely phrased it weirdly but owner's still have control over the accessibility of their mods, all they've really tried to add is legacy protection for collections (AKA mod packs) that require specific versions. As the policy of archiving, deleting or leaving old versions for download is far less standard on the Nexus than it is for other games, again Minecraft especially showcases that. EDIT: Actually the larger part of the problem is Vortex, if a mod is deleted on the site or locally it just deleted the installed copy of a mod. Breaking installs, if they added an argument in the code to stop the deployed mods being removed if the duplicate vortex moanaged install folder/site link was removed that would have also fixed it for collections. As modpack creators could provide version files as is from their master install.