So two days ago, my GOTY was running perfectly with the mods.. all of a sudden yesterday my computer restarted and not only did it randomly uninstall TW3GOTY but it’s also made the mods stop working...

And yes I’ve reinstalled the game through GOG Galaxy and tried manually installing basic mods like the medallion with the lit up eyes and they are just not applying.. I’ve tried to install them through nexus mod manage and even though they downloaded the mod would not apply in game. My PC knowledge is kind of exhausted.

Please send help!!

the world is a better place without galaxy. just drop galaxy. use classic installers.

First off, make sure you have only one game version installed. Not "The Witcher 3: Wild Hunt" AND "The Witcher 3: Wild Hunt - GOTY". If you have both versions, you can and should install it manually anyway.

Second, most Nexus Mods state that you have to, in fact, install them manually.
The reason is, as they most probably need a "MOD"-File AND a "DLC"-Update File.
The Nexus Mod Manager (so far) only creates a MOD-Folder (if not existent) and adds conent there, but he will leave out the "update" for the DLC-Folder.

Depending on what Mods you used or want to use, I can most probably help you out.

As just guessing here right now:
1. Do it by hand (Download the specific mods)
2. Open the Witcher Game (for Gog it is mostly in C:\Games\GOG Galaxy\Games\The Witcher 3 Wild Hunt)
=> Make sure to really use the version you actually have (GOTY has a different Link!)
3. Make sure you have a "Mods"-Folder here. If not, simply create the folder (name him: Mods) <- take care of the upper letter at the beginning, it is important to write it like this.
4. Put the file in the Mod-Folder, use winrar to get the items files and chose what you want
5. Make sure to check if there is any "dlc"-Update or Folder in there OR needed
6. Go back to your game folder and update the dlc folder with the implemented Mod-Update

Maybe this helps. For the most graphical Update to the witcher (such as the old witcher eyes etc.) I always saw a MOD-part and dlc-update.

Nexus Mod Manager never worked for Witcher 3 (any kind) for me. :(
Good luck.