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Either delete just the mod folder or delete everything and then reinstall everything, or at least the ones you know contains meshes.
It does actually. NMM having problems with proper installation and uninstallation of files is well known and some popular mods dont have a Download with Manager button specifically because they got sick of NMM doing that and then recieving error reports because of it. The problem with NMM is that it installs everything to the same location, so when you uninstall something it tries to run a check and see if any removed files were needed by another mod, and then reinstall the correct version of that file which doesnt always work the way thats its meant to.
MO is the only mod manager that is litterally incapable of leaving files hanging around because it installs everything completely seperate
You find those files in games\nexus mod manager\skyrim\install info.
That is why MO need to import that map when migrating from NMM.
By default, NMM places all files in to same folder:
<InstallationPath>\SteamApps\common\Skyrim\Data
Exactly where did it place those files for you and how recent version you were using?
Mod Organizer (YouTube playlist) by Gopher
https://www.youtube.com/playlist?list=PLE7DlYarj-DcLS9LyjEqOJwFUQIIQewcK