the message in the screenshot seems to me to indicate that you have gone wrong in your mod manager set up. it's not a false positive, whatever that means - its not lying to you. according to the data in the mod manager its confused as all hell because of the condition of the data in your folders and in the mod manager itself.
go back to the beginning - you're using vortex, yes? so you did what? download vortex, fire it up, and start pulling down mods and installing them?
what i think has happened is you've simply got old mods managed by your old mod manager in your mod directory. you need to clean that crap out of there before you can use any other mod manager.
if i were you i'd do this;
fire up vortex - purge everything.
fire up nmm - uninstall all the mods (don't delete the archives, just uninstall the mods).
fire up vortex - use it to purge all mods again.
go to your data folder - if it's got stuff in it then you've got random, unsupported mods in there that need to be removed. so, delete your data folder.
go to steam have it validate local files - this will rebuild a new, empty data folder.
you are now back in a vanilla configuration. game is ready to be played, no mods installed.
start a new game with no mods - make sure the game works before you do anything.
if you're happy that the game works, now you can mod it.
quit out, or alt f4 - whatever you need to do
go to vortex. set it up
- make sure your mod staging folder is on the same drive as your game but not inside the game folder.
- make sure your deployment method is hard link deployment
- your download folder can be anywhere - my preference is to have it on the same disk as my mod staging folder but thats just me
you should have your mods in a download folder somewhere, these are archive files, 7zip etc - you can drag them to vortex and install them or you can install from file via vortex. install a single mod - just one mod.
enable the mod and deploy the mod via vortex.
start your game - it should tell you mods are loaded. make sure that you see this message.
if the game starts up - you're on your way.
go back and repeat the process - but install your mods one at a time and deploy them one at a time - don't install 20-30 mods in one go as you will almost certainly get messages about missing masters and such.
when you have installed a few mods - start the game, make sure it works .... repeat repeat repeat.
if you get issues go to the vortex support page on nexusmods there are good people there who can help you - but if you clean your slate and start over you should be in a better position than you are currently.
oh and don't be tempted to use another mod manager while using vortex. going from one to another is an absolute guarantee that you'll wreck your game.
if all that sounds like too much effort nmm is still around and still being supported and you can go back to using that.
try this - see how you go.
oh and one final thing;
if you start a new game - start it with almost all mods disabled. you only want the smallest set of mods possible to start with. so i always have UFO4P, simsettlements 3-in-1, conqueror workshop framework and workshop plus enabled. everything else is disabled.
i get to the point where i am just about to leave the vault. i save and exit. this is my hard save point.
i load the game, exit the vault go to sanctuary and save before i trigger codsworth.
i go to vortex, enable the mods i want to play with, and reload the game.
i start the game do the quests with codsworth (or not), and bingo.
one word of warning - if you have creation club content - it has been known to absolutely muller the start of game quests - particularly the tunnel snakes content. i advise everyone to delete that nonsense out of their game files because it's really not very well tested and has caused no end of issues - its a personal choice, but my game is no better off for creation club content. YMMV.
