We've recently deployed CRM 2015 and Outlook and it seems we have our heads wrapped around tracking and set regarding except for this case:

In Outlook, conversations are turned on. When we reply to an email, CRM adds our tracking token to the subject of the reply email. Now the subject line of the reply and the one of the original email are different. Since the subjects are no longer the same, Outlook doesnt find both emails and display them as a conversation. You cant easily tell that there was a reply to the email in the Inbox without searching through the Sent folder.

Any way to address this? 

Hi,

In Outlook, the conversations are grouped by the Conversation IDs rather than the subject. Only messages with the same Conversations ID can be grouped as a conversation.

You can check the Conversation ID of a message by the tool MFCMAPI:

https://mfcmapi.codeplex.com/

If the Conversation ID is changed after CRM adds the tracking token to the email, this message will not be grouped as a conversation, and this is a CRM thing and we can do few in Outlook client side.

If you can confirm the Conversation ID is changed during the process above, I suggest you post the question in CRM forum:

https://social.microsoft.com/Forums/en-US/home?forum=crm

Regards,

Melon Chen
TechNet Community Su