Linked subgraphs are entirely broken

### Prerequisites

- [x] I am running the latest version of ComfyUI
- [x] I have searched existing issues to make sure this isn't a duplicate
- [x] I have tested with all custom nodes disabled ([see how](https://docs.comfy.org/troubleshooting/custom-node-issues#step-1%3A-test-with-all-custom-nodes-disabled))

### What happened?

Its been about 3 months since [this](https://github.com/Comfy-Org/ComfyUI_frontend/issues/5138) feature was taken away and it gets worse with each update since it gets neglected even further.

Subgraphs are no longer linked, no matter what is done. This used to work as if you duplicated a subgraph its inner subgraphs would be linked (last working version was 1.26.3) . There's no link anymore.

However if you give two nodes same "type" which is in the latest workflow save format (used to be node id) and manually edit the json file, you can make them linked. The issue is there's no way to give two subgraph nodes the same type within the current comfyui frontend.

Latest ui redesign is looking really nice and libraries would actually be extremely useful however we should be able to determine if an instance of a subgraph from the library is linked or not without having to manually edit the json file.

### Steps to Reproduce

1. create a subgraph
2. duplicate or copy/paste the subgraph
3. edit one of them and the other wont change

### How is this affecting you?

Feature doesn't work as expected

### ComfyUI Frontend Version

1.32.3

### Browser

Chrome/Chromium

### Console Errors

```javascript

```

### Logs

```shell

```

### Additional Context

_No response_

┆Issue is synchronized with this [Notion page](https://www.notion.so/Issue-6639-Linked-subgraphs-are-entirely-broken-2a56d73d36508192a7bac9dea2233e5c) by [Unito](https://www.unito.io)

Reproduce the issue in ComfyUI Frontend 1.32.3 by creating a subgraph, duplicating or copy/pasting it, and editing one instance. Trace the linked-subgraph duplication flow and the latest workflow save format; done means duplicated or library instances remain linked and reflect edits without manually editing JSON.

Written by the indexing model from the issue text.