Github connect ignores / deletes index.json

I have a store with theme which I developed and linked through github.
Also I have created another store, linked exact same branch and repo which connected to first store, but, when i connect it my main page is 404 and index.json is not in theme

What that could be? How I can fix that?

Hi Dima34,

That does sound unusual - have you set up any file ignore rules or config differences for the second store?

Hello! No gitignores. Just same github on different projects which behave differently

I found the problem:

My index.json on GitHub contained Shopify resouces path from my firs store ant that caused all problems and deleting index.json on my second store when i tried to load the theme there.

Removed all resources path and all works great!