Copy / pasting subgraphs yeilds strange results.

### Prerequisites

- [x] I am running the latest version of ComfyUI
- [x] I have custom nodes enabled

### What happened?

When copy / pasting subgraphs, it seems like the most recent copy isn't saving.

### Steps to Reproduce

1 - Create and build a subgraph, pop out to the main graph, ctrl + c to copy, then ctrl + v to paste a few copies.
2 - Go into the first copy of the subgraph and make a few changes.
3 - Pop out to the main graph and delete all other copies of the subgraph.
4 - Ctrl + c to copy the updated subgraph, then ctrl + v to paste a few copies.
5 - Save your workflow.

Observe:
Inpect the original subgraph and its copies. Changes revert back to the version that was created in step 1.

### How is this affecting you?

Feature doesn't work as expected

### ComfyUI Frontend Version

1.41.20

### Browser

Firefox

### Console Errors

```javascript

```

### Logs

```shell

```

### Additional Context

_No response_

┆Issue is synchronized with this [Notion page](https://www.notion.so/Issue-9976-Copy-pasting-subgraphs-yeilds-strange-results-3246d73d365081efbf7fff986b822243) by [Unito](https://www.unito.io)