Creating a message in an Inbox by Gmail thread via Gmai API

Question

Steps to reproduce:

1. Send a message from Inbox
2. Create a 2nd message in that same thread using Gmail API's "insert" method
3. Delete the first message either from the API or from Gmail (but really delete it, not just put it into trash)

Result: the 2nd message seems to get somehow disconnected from the thread and Inbox acts weirdly on it (see video if curious -- the weird behaviour itself starts at 2:10).

Bug or feature?

How to avoid it?