Since I've re-installed NMM a couple times, I think any other traces have been deleted when uninstalling and reinstalling. These are all my traces, I've been playing skyrim with the ".\stu" folder for like 2 weeks ago.
Mod(s) used: (I will provide if needed but don't think its relevant to the bug). I would like to try this method if it's feasible. I however don't know what files store these. Other than these two ways to solve the problem, I wanted to find exactly what files store the mod directory path for my skyrim so I can change it in the files instead of inside the application. I always run NMM as administrator and have tried looking at the security of all the folders that NMM deals with to make sure that there are no read/write permission problems. I click "Yes" to re-configure the path to the mod directory, and it just changed back to the ".\stu" path when it pops up the same initial setup window for all the mod directory paths. Before it even gets done loading the main mod list screen, it pops up a message saying that X mod is installed but could not be found in the mod directory. After the initial setup finds all games on my system and I select skyrim, it pops up a window asking for the path for mod directory and others, this is defaulted to the ".\Mods" path, so I continue. I've tried a complete re-install of NMM. I can restart NMM and go straight back into the settings/skyrim tab and see it has not updated at all. I've tried clicking the gear icon, selecting the skyrim tab, then replacing the ".\stu" path with the NMM default ".\Mods" path. I want to change the mod directory back to this default path but no matter how hard I try, I cannot change it. The original and default folder being the standard mod folder: 
I installed NMM before it became a community version probably ~4 years ago and had used a different mod directory path than the default:
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