If WhatsApp sends work but customer replies are missing from your Shopify inbox, the outbound and inbound paths have split. Sends go out through Meta's Cloud API. Replies come back through a separate route: Meta webhooks delivered to your app. Run one traceable test reply, rule out inbox filters first, and only then treat it as a connection problem for your app's support team.
Here's the situation I hear most: an order update arrives on the test phone, the customer replies "Can I change the address?", and nobody on the team sees it. Before anyone reconnects anything, work out which half is broken.
Why do sends work while replies go missing?
Because they don't share a pipe. When your app sends a template, it calls the Cloud API, and Meta returns delivery receipts to the app that sent the message. When a customer replies, Meta pushes that message to every app subscribed to the account through the messages webhook.
Meta requires an app to subscribe to each Messaging Account it wants webhooks from. If that subscription is missing or was removed, sends can still succeed while replies never arrive. If the app's receiving endpoint is down, Meta retries for up to 7 days, so replies may arrive late rather than never, and sometimes twice.
Step 1: send a reply you can trace
- From a phone you control, open the WhatsApp chat with your store.
- Check the sender number at the top matches the number connected in your app.
- Reply with something unique, like "TRACE 15:42 blue", and note the exact time.
- Wait two minutes.
Don't use a teammate's real customer conversation. You want one reply that only you could have sent.
Step 2: rule out the inbox before the connection
Most "missing" replies are sitting in a view nobody is looking at. In WhatFlow's Team Inbox:
- Clear the assignment filter. The Mine filter shows only chats assigned to you.
- Search all conversations for your trace phrase or the phone number.
- Check resolved or closed conversations. A customer replying to an old thread may land there.
- Ask a second agent to search too.
