Akimotori

Paths seems to be stored in C:\Users\<USERNAME>\AppData\Local\Black_Tree_Gaming\NexusClient.exe...\0.16.4.0\user.config -file, but I haven't edited it myself because I already did the other workaround described in my previous post above.

Well, I stumbled on this problem after I wanted to move my Steam-folder into another hard drive (SSD). Solution was to put Skyrim back where it was and then start Nexus Mod Manager and point the new location from the Settings -> Skyrim tab. PS. if you want to move Steam, don't delete your userdata-folder because it may contain screenshots etc. Despite this guide https://support.steampowered.com/kb_article.php?ref=7418-YUBN-8129 tells to delete all except the SteamApps folder and Steam.exe.