I have a scenario, where when case is created and auto-generated email is sent to customer that our agent will get back to in some time. Now if customer replies to email , those emails are not coming to salesforce and hence not getting attached to the respective case. Please help in capturing customer's reply as this is important.
You need to insert
Thread Id in Case Subject Or Body in the email template of that auto response rule. Also you need to set reply to address under auto response rule settings
When the Thread ID is missing in emails sent from cases, the response email will come back without the thread ID too. Without the Thread ID, the Salesforce system can't determine which case the email is related to, so the system treats it as a new email and creates a new case.
Also you need to set reply to address under auto response rule settings