extra_model_paths.yaml removed on update

### Custom Node Testing

- [x] I have tried disabling custom nodes and the issue persists (see [how to disable custom nodes](https://docs.comfy.org/troubleshooting/custom-node-issues#step-1%3A-test-with-all-custom-nodes-disabled) if you need help)

### Expected Behavior

loading all models from the paths listed in "extra_model_paths.yaml"

### Actual Behavior

the file "extra_model_paths.yaml" that finds models in different directories gets deleted from ComfyUI folder on each update, not sure it happaned before v0.3.62

### Steps to Reproduce

installing an update

### Debug Logs

```powershell
Adding extra search path checkpoints F:\ai\models\checkpoints
Adding extra search path vae F:\ai\models\vae
Adding extra search path clip F:\ai\models\clip
Adding extra search path clip_vision F:\ai\models\clip_vision
Adding extra search path diffusion_models F:\ai\models\diffusion_models
Adding extra search path text_encoders F:\ai\models\text_encoders
Adding extra search path configs F:\ai\models\configs
Adding extra search path controlnet F:\ai\models\controlnet
Adding extra search path embeddings F:\ai\models\embeddings
Adding extra search path loras F:\ai\models\loras
Adding extra search path upscale_models F:\ai\models\upscale_models
Adding extra search path unet F:\ai\models\unet
Adding extra search path custom_nodes C:\ComfyUI\custom_nodes
Adding extra search path download_model_base C:\ComfyUI\models
Adding extra search path custom_nodes C:\Users\***\AppData\Local\Programs\@comfyorgcomfyui-electron\resources\ComfyUI\custom_nodes
Setting output directory to: C:\ComfyUI\output
Setting input directory to: C:\ComfyUI\input
Setting user directory to: C:\ComfyUI\user
[START] Security scan
[DONE] Security scan
## ComfyUI-Manager: installing dependencies done.
** ComfyUI startup time: 2025-10-01 10:27:03.848
** Platform: Windows
** Python version: 3.12.11 (main, Aug 18 2025, 19:17:54) [MSC v.1944 64 bit (AMD64)]
** Python executable: C:\ComfyUI\.venv\Scripts\python.exe
** ComfyUI Path: C:\Users\***\AppData\Local\Programs\@comfyorgcomfyui-electron\resources\ComfyUI
** ComfyUI Base Folder Path: C:\Users\***\AppData\Local\Programs\@comfyorgcomfyui-electron\resources\ComfyUI
** User directory: C:\ComfyUI\user
** ComfyUI-Manager config path: C:\ComfyUI\user\default\ComfyUI-Manager\config.ini
** Log path: C:\ComfyUI\user\comfyui.log
[ComfyUI-Manager] Skipped fixing the 'comfyui-frontend-package' dependency because the ComfyUI is outdated.

Prestartup times for custom nodes:
1.8 seconds: C:\Users\***\AppData\Local\Programs\@comfyorgcomfyui-electron\resources\ComfyUI\custom_nodes\ComfyUI-Manager

Checkpoint files will always be loaded safely.
Total VRAM 32607 MB, total RAM 64909 MB
pytorch version: 2.8.0+cu129
Set vram state to: NORMAL_VRAM
Device: cuda:0 NVIDIA GeForce RTX 5090 : cudaMallocAsync
Using pytorch attention
Python version: 3.12.11 (main, Aug 18 2025, 19:17:54) [MSC v.1944 64 bit (AMD64)]
ComfyUI version: 0.3.62
[Prompt Server] web root: C:\Users\***\AppData\Local\Programs\@comfyorgcomfyui-electron\resources\ComfyUI\web_custom_versions\desktop_app
### Loading: ComfyUI-Impact-Pack (V8.22.2)
[Impact Pack] Wildcards loading done.
### Loading: ComfyUI-Impact-Subpack (V1.3.5)
[Impact Pack/Subpack] Using folder_paths to determine whitelist path: C:\ComfyUI\user\default\ComfyUI-Impact-Subpack\model-whitelist.txt
[Impact Pack/Subpack] Ensured whitelist directory exists: C:\ComfyUI\user\default\ComfyUI-Impact-Subpack
[Impact Pack/Subpack] Loaded 0 model(s) from whitelist: C:\ComfyUI\user\default\ComfyUI-Impact-Subpack\model-whitelist.txt
[Impact Subpack] ultralytics_bbox: C:\ComfyUI\models\ultralytics\bbox
[Impact Subpack] ultralytics_segm: C:\ComfyUI\models\ultralytics\segm
[Impact Subpack] ultralytics_bbox: C:\ComfyUI\models\ultralytics\bbox
[Impact Subpack] ultralytics_segm: C:\ComfyUI\models\ultralytics\segm
[C:\ComfyUI\custom_nodes\comfyui_controlnet_aux] | INFO -> Using ckpts path: C:\ComfyUI\custom_nodes\comfyui_controlnet_aux\ckpts
[C:\ComfyUI\custom_nodes\comfyui_controlnet_aux] | INFO -> Using symlinks: False
[C:\ComfyUI\custom_nodes\comfyui_controlnet_aux] | INFO -> Using ort providers: ['CUDAExecutionProvider', 'DirectMLExecutionProvider', 'OpenVINOExecutionProvider', 'ROCMExecutionProvider', 'CPUExecutionProvider', 'CoreMLExecutionProvider']
C:\ComfyUI\custom_nodes\comfyui_controlnet_aux\node_wrappers\dwpose.py:26: UserWarning: DWPose: Onnxruntime not found or doesn't come with acceleration providers, switch to OpenCV with CPU device. DWPose might run very slowly
warnings.warn("DWPose: Onnxruntime not found or doesn't come with acceleration providers, switch to OpenCV with CPU device. DWPose might run very slowly")

[rgthree-comfy] Loaded 48 epic nodes. 🎉

WAS Node Suite Error: There is no write access to `C:\ComfyUI\custom_nodes\was-ns` or `C:\ComfyUI\models`. Write access is required!
WAS Node Suite: OpenCV Python FFMPEG support is enabled
WAS Node Suite Warning: `ffmpeg_bin_path` is not set in `C:\ComfyUI\custom_nodes\was-ns\was_suite_config.json` config file. Will attempt to use system ffmpeg binaries if available.
WAS Node Suite: Finished. Loaded 220 nodes successfully.

"The biggest risk is not taking any risk. In a world that is changing quickly, the only strategy that is guaranteed to fail is not taking risks." - Mark Zuckerberg

### Loading: ComfyUI-Manager (V3.36)
[ComfyUI-Manager] network_mode: public
### ComfyUI Revision: UNKNOWN (The currently installed ComfyUI is not a Git repository)

Import times for custom nodes:
0.0 seconds: C:\Users\***\AppData\Local\Programs\@comfyorgcomfyui-electron\resources\ComfyUI\custom_nodes\websocket_image_save.py
0.0 seconds: C:\ComfyUI\custom_nodes\Comfyui-Resolution-Master
0.0 seconds: C:\ComfyUI\custom_nodes\comfyui-inpaint-cropandstitch
0.0 seconds: C:\ComfyUI\custom_nodes\comfyui-impact-subpack
0.0 seconds: C:\ComfyUI\custom_nodes\comfyui_ultimatesdupscale
0.0 seconds: C:\ComfyUI\custom_nodes\ComfyUI-segment-anything-2
0.0 seconds: C:\ComfyUI\custom_nodes\comfyui-kjnodes
0.0 seconds: C:\Users\***\AppData\Local\Programs\@comfyorgcomfyui-electron\resources\ComfyUI\custom_nodes\ComfyUI-Manager
0.0 seconds: C:\ComfyUI\custom_nodes\rgthree-comfy
0.1 seconds: C:\ComfyUI\custom_nodes\comfyui-advancedliveportrait
0.1 seconds: C:\ComfyUI\custom_nodes\comfyui-impact-pack
0.3 seconds: C:\ComfyUI\custom_nodes\nanobananaapi
0.3 seconds: C:\ComfyUI\custom_nodes\comfyui_controlnet_aux
1.1 seconds: C:\ComfyUI\custom_nodes\was-ns

[ComfyUI-Manager] default cache updated: https://raw.githubusercontent.com/ltdrdata/ComfyUI-Manager/main/alter-list.json
Failed to initialize database. Please ensure you have installed the latest requirements. If the error persists, please report this as in future the database will be required: (sqlite3.OperationalError) unable to open database file
(Background on this error at: https://sqlalche.me/e/20/e3q8)
[ComfyUI-Manager] default cache updated: https://raw.githubusercontent.com/ltdrdata/ComfyUI-Manager/main/model-list.json
Starting server

To see the GUI go to: http://127.0.0.1:8004
[ComfyUI-Manager] default cache updated: https://raw.githubusercontent.com/ltdrdata/ComfyUI-Manager/main/github-stats.json
[ComfyUI-Manager] default cache updated: https://raw.githubusercontent.com/ltdrdata/ComfyUI-Manager/main/extension-node-map.json
[ComfyUI-Manager] default cache updated: https://raw.githubusercontent.com/ltdrdata/ComfyUI-Manager/main/custom-node-list.json
comfyui-frontend-package not found in requirements.txt
comfyui-frontend-package not found in requirements.txt
[ERROR] An error occurred while retrieving information for the 'GGUFLoaderKJ' node.
Traceback (most recent call last):
File "C:\Users\***\AppData\Local\Programs\@comfyorgcomfyui-electron\resources\ComfyUI\server.py", line 633, in get_object_info
out[x] = node_info(x)
^^^^^^^^^^^^
File "C:\Users\***\AppData\Local\Programs\@comfyorgcomfyui-electron\resources\ComfyUI\server.py", line 595, in node_info
return obj_class.GET_NODE_INFO_V1()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\***\AppData\Local\Programs\@comfyorgcomfyui-electron\resources\ComfyUI\comfy_api\latest\_io.py", line 1315, in GET_NODE_INFO_V1
schema = cls.GET_SCHEMA()
^^^^^^^^^^^^^^^^
File "C:\Users\***\AppData\Local\Programs\@comfyorgcomfyui-electron\resources\ComfyUI\comfy_api\latest\_io.py", line 1440, in GET_SCHEMA
schema = cls.FINALIZE_SCHEMA()
^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\***\AppData\Local\Programs\@comfyorgcomfyui-electron\resources\ComfyUI\comfy_api\latest\_io.py", line 1431, in FINALIZE_SCHEMA
schema = cls.define_schema()
^^^^^^^^^^^^^^^^^^^
File "C:\ComfyUI\custom_nodes\comfyui-kjnodes\nodes\model_optimization_nodes.py", line 1932, in define_schema
io.Combo.Input("model_name", options=[x for x in folder_paths.get_filename_list("unet_gguf")]),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\***\AppData\Local\Programs\@comfyorgcomfyui-electron\resources\ComfyUI\folder_paths.py", line 355, in get_filename_list
out = get_filename_list_(folder_name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\***\AppData\Local\Programs\@comfyorgcomfyui-electron\resources\ComfyUI\folder_paths.py", line 316, in get_filename_list_
folders = folder_names_and_paths[folder_name]
~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^
KeyError: 'unet_gguf'

FETCH ComfyRegistry Data: 5/98
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FETCH ComfyRegistry Data: 95/98
FETCH ComfyRegistry Data [DONE]
[ComfyUI-Manager] default cache updated: https://api.comfy.org/nodes
FETCH DATA from: https://raw.githubusercontent.com/ltdrdata/ComfyUI-Manager/main/custom-node-list.json [DONE]
[ComfyUI-Manager] All startup tasks have been completed.
```

### Other

_No response_