Do I need to manually update my CRM for Transitioned conversations?

Yes.

To give some clarity around this, we've changed transition notifications to specifically mark messages where we didn't extract data. So for example in this transition email:

You can see that data was not extracted from the message "Actually, sorry but I need to cancel ASAP." So, that information will need to be manually entered in to your CRM. 

Basically, for any message that is marked with "data was not extracted from this message" you will need to manually update your CRM with any new data that came from that message.