App dev command breaks storefront access tokens (irreversible)

I just used shopify app dev and it broke all my graphql calls to the storefront API from my app theme extensions. Even after running shopify app dev clean everything is still broke.

All storefront API calls result in 403 even though I’m sending along a specific storefront token for a given merchant:

{
    "errors": [
        {
            "message": "Channel not found for the given token.",
            "extensions": {
                "code": "ACCESS_DENIED"
            }
        }
    ]
}

I’ve tested this by accessing a different dev store, everything was working. I ran shopify app dev for that specific and the same error occurs. Also tried shopify app dev clean again, but still getting the same error.

I think I discovered the issue. This app is using a legacy flow, but the app .toml did not have use_legacy_install_flow set. This has never been a problem, but it looks like this has changed and caused some scopes to reset?

Once I added:

[access_scopes]
use_legacy_install_flow = true

I triggered the oauth flow and the issue was resolved.