I finally fixed the error definitely, I think. You have to manually delete the plugins.txt archive. This will cause all your mods (.esp and .esm, including skyrim.esm) to be deactivated. You must now open the launcher, which will generate a new plugins.txt, fixed. Finally, you have to manually activate your mods and .esm and .esp again. I did it on the Nexus Mod Manager, not on the launcher, but it should be the same. Now when you activate a mod it no longer adds a skyrim.esm. In fact, in plugins.txt, skyrim.esm is not on the list. But it works and is activated.
