Why is the upgraded Shopify Checkout Extensibility asking for login again?

We have a mobile app with checkout page in web view. Had no issues until upgrading checkout to Shopify Checkout Extensibility. After that checkout page is asking for login for already logged in users. Custom header “X-Shopify-Customer-Access-Token” is already present while calling checkout url. Adding the query used to get checkout url

query checkoutURL {
cart(id: cartId) {
checkoutUrl
}
}