If you have a workspace like this:
- main repository
    - other repository

If you add that other repositories folder to your workspace, in `.code-workspace` VSC will place the following:
```
"folders": [
    {
        "path": "."
    },
    {
        "path": "very\\nice\\sub-folder"
    }
]
```

VSC somehow decides to stop looking for the other repositories after it found one in the path `.` AKA your root folder.

So simply putting the root folder underneath your subfolders will fix it.

Like so:
```
"folders": [
    {
        "path": "very\\nice\\sub-folder"
    },
    {
        "path": "."
    }
]
```