I think i found a solution (I cant promise that this will work for everyone and that it will not cause more problems since i am not an expert on this but it did work for me).
I found where the mods are from the NMM client and then closed the NMM client.
I went to D:\Games\Nexus Mod Manager\Skyrim\Mods and copied all the mods.
Pasted the mods to a new folder.
Then deleted the mods from D:\Games\Nexus Mod Manager\Skyrim\Mods.
I went to D:\Games\Nexus Mod Manager\Skyrim\Mods\cache.
Copied all the files from there to a second new folder.
Then deleted the files from D:\Games\Nexus Mod Manager\Skyrim\Mods\cache.
Now i went and opened the NMM client and when it asked if i moved the mods folder i pressed no on it.
After that was done and NMM client was open i saw that there were 0 mods downloaded/installed which is what i expected.
Then i closed the NMM client.
I went back to D:\Games\Nexus Mod Manager\Skyrim\Mods\ and pasted all the mods there from the first folder i made.
Next i went to D:\Games\Nexus Mod Manager\Skyrim\Mods\cache and pasted all the files from the second folder i made.
Then i opened NMM client and everything was working. I have not had problems for the 10 minutes of play testing i did.
Sorry if this was badly written. (also was what i did basically uninstalling and reinstalling the mods?)
October 2020, and I can confirm that this still works for me