Added the id headers from message and resolved the issue.
Why reference headers can be set as custom headers in graph client Message class? Also I tried graph explorer for reply a mail using message id but got 400 as response Showing runtime application error?
To send the reply for a email, headers like references, reply-to is required to get the chronological order of thread. I tried to add these headers manually via graph client but I can set these headers only as custom headers in internetMessageHeaders in message class. Also it is taken as custom headers so the reply sent from other providers didn't consider these custom headers. So email sent from them don't have the headers value correctly. I also tried SingleValueExtendedProperty but couldn't get these in headers.
Tried graph explorer with the request for sending reply
https://graph.microsoft.com/v1.0/me/messages/{id}/reply
but I got 400 as response.
Thanks in advance for your valuable suggestions.