Missing links when saving

### 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

Saving a workflow works.

[image_flux2_klein_image_edit_9b_base.json](https://github.com/user-attachments/files/26093662/image_flux2_klein_image_edit_9b_base.json)

### Actual Behavior

When saving a workflow, some links are missing.

### Steps to Reproduce

- Open template for Image Flux2 Klein Image Edit 9B.
- Save the workflow.
- Open it again.

Some links for the 'Reference Conditioning' are missing.

### Debug Logs

```powershell
Adding extra search path checkpoints L:\StabilityMatrix\Data\Models\StableDiffusion
Adding extra search path diffusers L:\StabilityMatrix\Data\Models\Diffusers
Adding extra search path loras L:\StabilityMatrix\Data\Models\Lora
Adding extra search path loras L:\StabilityMatrix\Data\Models\LyCORIS
Adding extra search path clip L:\StabilityMatrix\Data\Models\TextEncoders
Adding extra search path clip_vision L:\StabilityMatrix\Data\Models\ClipVision
Adding extra search path embeddings L:\StabilityMatrix\Data\Models\Embeddings
Adding extra search path vae L:\StabilityMatrix\Data\Models\VAE
Adding extra search path vae_approx L:\StabilityMatrix\Data\Models\ApproxVAE
Adding extra search path controlnet L:\StabilityMatrix\Data\Models\ControlNet
Adding extra search path controlnet L:\StabilityMatrix\Data\Models\T2IAdapter
Adding extra search path gligen L:\StabilityMatrix\Data\Models\GLIGEN
Adding extra search path upscale_models L:\StabilityMatrix\Data\Models\ESRGAN
Adding extra search path upscale_models L:\StabilityMatrix\Data\Models\RealESRGAN
Adding extra search path upscale_models L:\StabilityMatrix\Data\Models\SwinIR
Adding extra search path hypernetworks L:\StabilityMatrix\Data\Models\Hypernetwork
Adding extra search path ipadapter L:\StabilityMatrix\Data\Models\IpAdapter
Adding extra search path ipadapter L:\StabilityMatrix\Data\Models\IpAdapters15
Adding extra search path ipadapter L:\StabilityMatrix\Data\Models\IpAdaptersXl
Adding extra search path prompt_expansion L:\StabilityMatrix\Data\Models\PromptExpansion
Adding extra search path ultralytics L:\StabilityMatrix\Data\Models\Ultralytics
Adding extra search path ultralytics_bbox L:\StabilityMatrix\Data\Models\Ultralytics\bbox
Adding extra search path ultralytics_segm L:\StabilityMatrix\Data\Models\Ultralytics\segm
Adding extra search path sams L:\StabilityMatrix\Data\Models\Sams
Adding extra search path diffusion_models L:\StabilityMatrix\Data\Models\DiffusionModels
[START] Security scan
[DONE] Security scan
** ComfyUI startup time: 2026-03-18 18:07:14.165
** Platform: Windows
** Python version: 3.12.12 (main, Feb 3 2026, 22:54:57) [MSC v.1944 64 bit (AMD64)]
** Python executable: L:\StabilityMatrix\Data\Packages\ComfyUI\venv\Scripts\python.exe
** ComfyUI Path: L:\StabilityMatrix\Data\Packages\ComfyUI
** ComfyUI Base Folder Path: L:\StabilityMatrix\Data\Packages\ComfyUI
** User directory: L:\StabilityMatrix\Data\Packages\ComfyUI\user
** ComfyUI-Manager config path: L:\StabilityMatrix\Data\Packages\ComfyUI\user\__manager\config.ini
** Log path: L:\StabilityMatrix\Data\Packages\ComfyUI\user\comfyui.log
L:\StabilityMatrix\Data\Packages\ComfyUI\venv\Lib\site-packages\requests\__init__.py:113: RequestsDependencyWarning: urllib3 (2.6.3) or chardet (7.0.1)/charset_normalizer (3.4.6) doesn't match a supported version!
warnings.warn(
[PRE] ComfyUI-Manager
L:\StabilityMatrix\Data\Packages\ComfyUI\venv\Lib\site-packages\torch\cuda\__init__.py:65: FutureWarning: The pynvml package is deprecated. Please install nvidia-ml-py instead. If you did not install pynvml directly, please report this to the maintainers of the package that installed pynvml for you.
import pynvml # type: ignore[import]
WARNING: You need pytorch with cu130 or higher to use optimized CUDA operations.
Found comfy_kitchen backend cuda: {'available': True, 'disabled': True, 'unavailable_reason': None, 'capabilities': ['apply_rope', 'apply_rope1', 'dequantize_nvfp4', 'dequantize_per_tensor_fp8', 'quantize_mxfp8', 'quantize_nvfp4', 'quantize_per_tensor_fp8']}
Found comfy_kitchen backend triton: {'available': False, 'disabled': True, 'unavailable_reason': "ImportError: No module named 'triton'", 'capabilities': []}
Found comfy_kitchen backend eager: {'available': True, 'disabled': False, 'unavailable_reason': None, 'capabilities': ['apply_rope', 'apply_rope1', 'dequantize_mxfp8', 'dequantize_nvfp4', 'dequantize_per_tensor_fp8', 'quantize_mxfp8', 'quantize_nvfp4', 'quantize_per_tensor_fp8', 'scaled_mm_mxfp8', 'scaled_mm_nvfp4']}
Checkpoint files will always be loaded safely.
Total VRAM 12288 MB, total RAM 32527 MB
pytorch version: 2.10.0+cu126
Set vram state to: LOW_VRAM
Device: cuda:0 NVIDIA GeForce RTX 3060 : cudaMallocAsync
Using async weight offloading with 2 streams
Enabled pinned memory 14637.0
working around nvidia conv3d memory bug.
Using pytorch attention
aimdo: src-win/cuda-detour.c:77:INFO:aimdo_setup_hooks: found driver at 00007FF9D5C10000, installing 4 hooks
aimdo: src-win/cuda-detour.c:61:DEBUG:install_hook_entrys: hooks successfully installed
aimdo: src/control.c:69:INFO:comfy-aimdo inited for GPU: NVIDIA GeForce RTX 3060 (VRAM: 12287 MB)
DynamicVRAM support detected and enabled
Python version: 3.12.12 (main, Feb 3 2026, 22:54:57) [MSC v.1944 64 bit (AMD64)]
ComfyUI version: 0.17.0
comfy-aimdo version: 0.2.12
comfy-kitchen version: 0.2.8
ComfyUI frontend version: 1.41.20
[Prompt Server] web root: L:\StabilityMatrix\Data\Packages\ComfyUI\venv\Lib\site-packages\comfyui_frontend_package\static
Asset seeder disabled
[START] ComfyUI-Manager
### Loading: ComfyUI-Manager (V4.1)
[ComfyUI-Manager] network_mode: public
### ComfyUI Version: v0.17.0-34-gb941913f | Released on '2026-03-17'
[ComfyUI-Manager] default cache updated: https://raw.githubusercontent.com/Comfy-Org/ComfyUI-Manager/main/model-list.json
[ComfyUI-Manager] default cache updated: https://raw.githubusercontent.com/Comfy-Org/ComfyUI-Manager/main/alter-list.json
[ComfyUI-Manager] default cache updated: https://raw.githubusercontent.com/Comfy-Org/ComfyUI-Manager/main/github-stats.json
[ComfyUI-Manager] Legacy UI is enabled.
[ComfyUI-Manager] default cache updated: https://raw.githubusercontent.com/Comfy-Org/ComfyUI-Manager/main/custom-node-list.json
[ComfyUI-Manager] default cache updated: https://raw.githubusercontent.com/Comfy-Org/ComfyUI-Manager/main/extension-node-map.json
Skipping loading of custom nodes
Context impl SQLiteImpl.
Will assume non-transactional DDL.
Starting server

To see the GUI go to: http://127.0.0.1:8188
FETCH ComfyRegistry Data [DONE]
[ComfyUI-Manager] default cache updated: https://api.comfy.org/nodes
FETCH DATA from: L:\StabilityMatrix\Data\Packages\ComfyUI\user\__manager\cache\1514988643_custom-node-list.json [DONE]
[ComfyUI-Manager] All startup tasks have been completed.
```

### Other

_No response_