After a lot of trial and error, I have stumbled across a solution that has the potential to be a massive headache if a lot of your conversation threads and contacts are affected by this. Here’s how I fixed it on my Google Nexus 6:
- In the Hangouts app, navigate to Settings > SMS. Ensure that the “Default SMS messaging account” is correct. For some reason, mine got switched to “SMS only” in the course of switching back and forth between Hangouts and Messenger for SMS.
- Next, open an SMS thread from one of the affected contacts. Select the menu icon in the upper right corner, and then select Un-merge SMS.
- Go back, and long press the Hangouts conversation and the SMS conversation for that contact. The “merge” option should again appear in the upper right.
Unfortunately, this option will only fix two out of the three potential conversation threads – you can merge Hangouts and SMS, for instance, but Google Voice will still appear separately.
Hopefully Google fixes this problem very soon.