The new token-based threading is now supported from automated emails too. Placing a threading token in the email’s subject or body will securely link email replies to the correct record. If the related record is a case, Email-to-Case processes email replies automatically. To process incoming emails containing threading tokens for non case objects, create an Apex Email Service and use the EmailMessages.getRecordIdFromEmail function to find the record that matches the token
How: Go to the Send Email core action in Flow Builder. When you’re setting input values, choose to add a threading token to the email subject or body. Be sure to include a Related Record ID.

