The Vortex Guide to not using Vortex (V2.0) - Mod Rescue
This is more about how to save your Mod Collections that you downloaded though Nexus Mods, you will need to make the move to MO2 for this to work (the only one i know of), and The Guide to The way to not use Vortex will be at the bottom. This guide is not about getting Vortex Working. it about using it as a Mod Downloader only, this is for their Vortex only Collections.
If Vortex is Bricked and your mod collection is locked away and uninstalling Vortex is the only way forward you can save your collection by pulling your Staging Folder and your Downloads Folder from their current spot to a HDD drive or your storage drive. if you have not created and linked these folders letting Vortex auto do it they will be in different spots.
If Vortex created your Folders then Both Folder will be in a hidden folder, the Roaming Folder.
To get here you will hit the Windows Key (between Ctrl and Alt) + R. will bring up a search bar the type %appdata% click ok then go to vortex > Games > Mods . This should be your Staging folder and Downloads folder to a HDD drive is fine.
Moving these will make Vortex lose track and uninstalling Vortex will not take your collection away if your Games folder still has old vortex hard linked mods in it you can always delete the Data folder and revivify it though Steam or GOG.
Then you Install MO2 create a profile for these lost links and link MO2 file locations to these moved folders. a MO2 Query info will be needed to relink the mods to Nexus Mods.
the lower part goes though file placement or organization.
You should be good to go.
- ~The Guide to not using Vortex~
If you want to use the Nexus Mods Collection this can be done with a mix of Vortex and MO2. when installing Vortex i would put everything on a HDD drive away from the games your Moding. Vortex, the Staging Folder, and The Downloads Folder.
You create 2 Folders name one (This Game) Staging Folder (Fallout 4 Staging Folder) and the other (This Games) Zipped Mods, the Download Folder (Fallout 4 Zipped Folder) and then you link them though Vortex's Setting as long as the mods you download end up in these folders correctly your good never to look at vortex again. Moving these file way from where they were link will make vortex loses track of the mods wich is fine. after move the folders away delete all the mods and its archive in vortex. but you must move the folders first or vortex will delete them.
- if you want it to look cleaner you could always create a master folder and call it the Staging Folder and another one and call it Downloads Folder (Zipped Folder) and your Game own folders for Fallout 4 Staging and Fallout 4 Zipped Folders and move them into the Staging Folder or Zipped Folder.
- if you want a faster game load in speed you can move your Staging Folder to your SSD where your game is stored and your Zipped Folders can be keept on any HDD Storage Drive but with MO2 its fine if both are left in a HDD Drive.
- You could also create staging and Download folders for spacfic collections like Fallouts Tale of Two Wastelands > TTW Staging Folder , and TTW Zipped Folder > Link them in vortex> download the collection> as long as all the mods go into these folders correctly > then put the folders in the Staging and Downloads Folder locking out vortex. and then you would link MO2 to each of the respective folders. once done your delete all the mods in vortex to start a clean.
Download MO2 - From one of there many guides or https://github.com/Modorganizer2/modorganizer/releases
Creating Your MO2 Mods Collection Profile and Linking this way you will need revivified though mo2. and if you’re like a mod it can always be manually moved mods into MO2 own Staging and Downloading Folders and get rid of vortex.
You don't want vortex to touch any of your games and should be separated in this way.
After MO2 revivified and takes ahold of the Load order you can update though MO2 normally.
If your Mod has and install setup asking for diffrent setting at download and you wish to change these setting it this will require a redownload from MO2.
The stand alone Loot mod https://loot.github.io/ is needed for MO2 to have a better automated system.
all Script Extenders or anything that need to be placed in the Steam or GOG Games Folders along side the .exe needs to be manualy installed and placed.
I'm sorry if this doesn't help you but i do wish you the best of luck. as this suck and even more so if you paid for it.