I looked and could not find this topic, although I did find an old one similar to this involving Baldur's Gate 3.
What is happening is that I built a new Skyrim AE game changing mods from the previous one, eliminating some and adding others. The game loaded up properly, but it added back old mods I had disabled for this run through. For example, I turned off More Kats Skyrim, but kats are everywhere. I turned off Auri (Song of the Green) but there's her pod on the map.
So I disabled them again in the plugins section (they were enabled again in Vortex), loaded the game, which told me a bunch of mods were now not present, and played. Things were fine, until I reloaded the next day, and there they were again, all loaded up.
So I went into the Mods section of Vortex, so theoretically they could not load. Same thing happened, though: on a second load up they were all back again despite being disabled in the mods section.
I have never seen this before, its new to me with Vortex. Its always worked so well, I cannot understand what its doing.