Cannot Find Contents of data folder in Normal File Explorer - Skyrim Special Edition

[CayugaDuck]

Recently, starting in Feburary 13, 2025, had CTD issues with my Skyrim Special Edition modded instances through MO2, and when I was troubleshooting, I deleted and reinstalled my whole game, which seems to have caused a weird disconnect between the game's Data folder and the data folder MO2 calls for. For some reason, when searching for the Data folder through the normal file explorer on my computer, the folder is devoid of any files relating to my mods, other MO2 applications, and even SKSE. What's the strangest part is that if I open the data folder via MO2's "Explore Virtual Folder" feature, all of the files are still there and appear to, for the most part, be working properly. I only noticed an issue when attempting to load my saved racemenu presets and the majority if them didn't show up in-game. Checking the CharGen folder through the "Explore Virtual Folder" function shows that my presets are mostly gone for some reason. Even when I restored them from a backup save I had, they seemed to be reset after loading another save/instance. 

I tried copying the data files from the Explore Virtual Folder menu and pasting them back into my file explorer data files, and it said that I was trying to paste the the same directory and there was nothing to paste. I also tried making a copy of the Explore Virtual Folder data folder onto my desktop, but when it finished, it appeared the same as my data folder when viewed via my regular file explorer: none of the MO2 or modded files were there.

I will note that I do have a backup of my entire Skyrim Special Edition folder from February 13, assumedly before I reinstalled the game, and the data folder appears to be intact. Should I restore my current data folder from this backup? I don't want to do anything rash before I have a better idea what is going on. 

Here are screenshots of the data folder through my file explorer, and the data folder through Explore Virtual Folder:

I am very confused why this is, and why there is a disconnect between the data folders, and why the game seems to work even though I can't see any of the proper files on my computer. Please advise!

 

 

[GSDFan]

  On 4/1/2025 at 4:54 PM, CayugaDuck said:

Recently, starting in Feburary 13, 2025, had CTD issues with my Skyrim Special Edition modded instances through MO2, and when I was troubleshooting, I deleted and reinstalled my whole game, which seems to have caused a weird disconnect between the game's Data folder and the data folder MO2 calls for. For some reason, when searching for the Data folder through the normal file explorer on my computer, the folder is devoid of any files relating to my mods,

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This is normal behavior for MO2. MO2 strives to keep the games folder and data folder clean from the mods installed and activated in the left mods pane. When an executable is run from within MO2 it uses its virtual file system, VFS, to present those files to the game. 

  On 4/1/2025 at 5:27 PM, CayugaDuck said:

I was speaking with a friend who also does modding, and he mentioned how MO2 tends not to save the modded files directly in the base data folder, and that each instance has its own set of file directories. Is this true?

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Yes this is true.

 

  On 4/1/2025 at 5:27 PM, CayugaDuck said:

each instance has its own set of file directories

Expand  

Settings / paths.

Your "Base Directory" is the home location of your instance. Depending on how you did your install it may contain the Downloads, Mods, Caches, Profiles and the Overwrite mod, and yes it is a folder but MO2 refers to it as a mod. It can also contain the MO2 related files.

Use the folder icon on the toolbar to access all of your folders.

[z929669]

The MO VFS can only reveal actual files on your system. Those files are just mapped onto an analog of the actual game path from the 'real' file locations (Downloads, Mods, Cache, Profile, and Overwrite).

The reason you don't see all these folders in the actual game directory is because they are compressed inside the game's *.BSA files. If you extract every BSA, you get this:

... these paths reside under your game Data directory but inside the BSAs. MO shows more, because each mod has it's own assets, and they are all combined in the VFS exlporer. Think of the VFS as soft links to real files in non-game real locations that are mapped onto the virtualized game path.

Incidentally, Windows 11 has some bugs with the MO VFS, but they don't seem to affect me to any noticeable degree. I don't know the specifics.

---

My example. My modded game working as expected (launch via MO), and base game works as expected if I launch via Steam (no mods this way though):

[CayugaDuck]

  On 4/1/2025 at 4:54 PM, CayugaDuck said:

Recently, starting in Feburary 13, 2025, had CTD issues with my Skyrim Special Edition modded instances through MO2, and when I was troubleshooting, I deleted and reinstalled my whole game, which seems to have caused a weird disconnect between the game's Data folder and the data folder MO2 calls for. For some reason, when searching for the Data folder through the normal file explorer on my computer, the folder is devoid of any files relating to my mods, other MO2 applications, and even SKSE. What's the strangest part is that if I open the data folder via MO2's "Explore Virtual Folder" feature, all of the files are still there and appear to, for the most part, be working properly. I only noticed an issue when attempting to load my saved racemenu presets and the majority if them didn't show up in-game. Checking the CharGen folder through the "Explore Virtual Folder" function shows that my presets are mostly gone for some reason. Even when I restored them from a backup save I had, they seemed to be reset after loading another save/instance. 

I tried copying the data files from the Explore Virtual Folder menu and pasting them back into my file explorer data files, and it said that I was trying to paste the the same directory and there was nothing to paste. I also tried making a copy of the Explore Virtual Folder data folder onto my desktop, but when it finished, it appeared the same as my data folder when viewed via my regular file explorer: none of the MO2 or modded files were there.

I will note that I do have a backup of my entire Skyrim Special Edition folder from February 13, assumedly before I reinstalled the game, and the data folder appears to be intact. Should I restore my current data folder from this backup? I don't want to do anything rash before I have a better idea what is going on. 

Here are screenshots of the data folder through my file explorer, and the data folder through Explore Virtual Folder:

I am very confused why this is, and why there is a disconnect between the data folders, and why the game seems to work even though I can't see any of the proper files on my computer. Please advise!

 

 

Expand  

Some more information that may be important:

I was speaking with a friend who also does modding, and he mentioned how MO2 tends not to save the modded files directly in the base data folder, and that each instance has its own set of file directories. Is this true? They also mentioned that what I was used to may have been a leftover from when I used Vortex instead of MO2, which puts all the modded folders directly into the base data folder. So, perhaps what I was used to was a leftover of Vortex (such as the presets being universal instead of per-instance), and when I reinstalled the game, it got rid of those old Vortex file directories I was using, not knowing that it was leftover from then. Am I correct?

[CayugaDuck]

 

  On 4/2/2025 at 12:03 AM, z929669 said:

The MO VFS can only reveal actual files on your system. Those files are just mapped onto an analog of the actual game path from the 'real' file locations (Downloads, Mods, Cache, Profile, and Overwrite).

The reason you don't see all these folders in the actual game directory is because they are compressed inside the game's *.BSA files. If you extract every BSA, you get this:

... these paths reside under your game Data directory but inside the BSAs. MO shows more, because each mod has it's own assets, and they are all combined in the VFS exlporer. Think of the VFS as soft links to real files in non-game real locations that are mapped onto the virtualized game path.

Incidentally, Windows 11 has some bugs with the MO VFS, but they don't seem to affect me to any noticeable degree. I don't know the specifics.

---

My example. My modded game working as expected (launch via MO), and base game works as expected if I launch via Steam (no mods this way though):

Expand  

Great, this makes sense. Thanks for informing me! I'm glad to learn that MO2 acts this way so I don't get confused again in the future.

  On 4/1/2025 at 8:59 PM, GSDFan said:

This is normal behavior for MO2. MO2 strives to keep the games folder and data folder clean from the mods installed and activated in the left mods pane. When an executable is run from within MO2 it uses its virtual file system, VFS, to present those files to the game. 

Yes this is true.

 

Settings / paths.

Your "Base Directory" is the home location of your instance. Depending on how you did your install it may contain the Downloads, Mods, Caches, Profiles and the Overwrite mod, and yes it is a folder but MO2 refers to it as a mod. It can also contain the MO2 related files.

Use the folder icon on the toolbar to access all of your folders.

Expand  

Yes, I understand now. Thank you very much. This clears everything up for me. It's also good to now be aware of how to access the file paths if I ever need to. Much appreciated for your help, once again!

Edited Wednesday at 03:35 PM by CayugaDuck

[GSDFan]

No problem, That is why STEP is here. It is not only a modding guide for various games, but a repository of knowledge on what is needed to do it. Without the participation of the community it will never expand on that knowledge. 

All users from beginners to experts are treated a equals and with respect and welcome to ask questions no matter how simple or complex they are.