Board Thread:Mod Discussion/@comment-122.59.206.67-20150819065951/@comment-6881629-20150821121011

NMM downloads mods to their own folder then when you activate them it extracts the files to Skyrim it logs all files from the mod and makes back ups of any files that are changed or replaced by the mod (so then if you deactivate them any changes are fully undone), it needs to be installed before the mods you really have to unistall everything and start again install Skyrim then NMM and finally the mods for it to work as it was meant to.

You might be able to get the mods working by just downloading them with NMM again and activating them with NMM but it probably wouldn't be able to remove mods as cleanly as could if it was installed in the right order.