The plugins are all active and working like normal as well, but I can't get the NMM to see all of my mods that I said 'no' to download the latest version to. Hey so ive been searching the internet for a little while here and found no one in having quite the problem i.
Like I said before, I checked the cache and mod folder and all of my mods are still there. Debug console from nexus mods not working for me. Since I did not want to at the time I said 'no' and now find that after doing this all of the out-of-date mods were completely removed from under the 'mods' tab in NMM. When I came back to it later (after finally being able to connect to the online account) I got a lot of popups asking about downloading the latest versions of my mods. 48.2 and originally when i first downloaded the latest version and installed it, all of my mods showed up.
I had to reinstall the NMM because I had a version that was below the version that supports updates.
I'm having this same problem, only my mods are still in the mods folder of the NMM.