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Because at first guess its sounding like the mod ESLs/ESMs are disabled and need to be enabled. The way you go about that changes with the tool...
A couple things you can try are:
-Go to Steam>Settings>Downloads>Clear Download cache (clear cache). Doing this is harmless and tends to resolve bogus update issues. Test to see if your mods are working.
-Go to C/...Users/you/Appdata/Local/Fallout 4 and check in the .txt files (it will either be called DLCList.txt or Plugins.txt - SkyrimSE uses Plugins.txt, but I'm not sure FO4 is the same). Open them and look for your mods' names. If they DON'T have an asterisk * in front of the name, try adding one-this was one of the ways to force the mod handler in SkyrimSE to recognize a mod. If this doesn't work, undo whatever changes you make and I'm out of ideas.
Note: Bethesda's in-game mod handlers are crappy tools for properly managing your mods, especially as your lists get longer. Once you start trying to run more than say 10 mods you might want to start using third-party managers such as Vortex or MO2 (which is what I use) because they give you much better control over your mods and don't make a mess of your game folders. Vortex even has an extension to import bethesdanet mods for proper handling.
also make sure you're not over the plugin limit. I don't remember what it is but I want to say 255 esp/esm files. I only say that because the only time I've had mods disable themselves is when I was over the limit or if I didn't launch the game with the f4se loader
the one and only Nexus Mod Manager
i cleared the download cache and i checked the plugin txt file, i noticed that the mods that systematically gets disabled are simply not mentioned there. no wonders it doesn't work lmao
Zekerian uses that and would know, she'll be around soon (usually)
i checked the zip files and they're all where they should be, plus reinstalling the mods, yet somehow i end up at square one with the same few mods being deactivated the minute i boot up the game. what kind of wizard am i even fighting here
If you decide to switch managers I suggest
-saving all of your .zip mod downloads to a safe location so you won't need to download them again (you can use those .zip files with your new manager later) and
-Doing a full, clean reinstallation of your game. In the long run you will be much happier without old files lurking around fouling things up.
Are they all suited to the specific build of your game? Is your game Next Gen, or Downgraded/not updated?
F4SE MUST BE UPDATED TO THE CORRECT VERSION and you should always launch using F4SE, not a mod organizer or the steam play button.
If you're using a DOWNGRADED version of the game, you *cannot use CC mods* since they require you to have access to them. You can slip them into your mod folder somehow but I don't use them - other people describe how to do that.
If you're starting the game in any way other than using F4SE on your desktop WHILE STEAM HAS ALREADY BEEN LAUNCHED, you need to do that. launch steam, fully wait for it to run.
THEN launch f4se.
Making sure your mods are all correct is the more important factor if you're "losing" some of them. Are they updated or not? They *must* match your game version.
i uninstalled NMM and installed Vortex, casually reinstalling all my mods back there, some had missing ESP files so like any normal human being would've done i checked what's the issue.
.turns out i didn't had the next gen update and had updated mods for that specific update which was clearly nonexistent so it messed up everything
so i went in steam, Fallout 4 'properties', 'installed files' and 'verify integrity of game files' which had 60~ missing files (yeouch), and then i booted F4 via F4SE Loader and now the game functions as intended
well, aside from that, thank you all for your patience and for the crucial infos you have given me so far