Q: iMessages and messages no longer linked

I had to update my appleid a while back because the email address I was using, I no longer use. This caused a huge amount of problems and I've fixed most of them. I'm left with iMessages on the desktop and messages no longer working together. I used to be able to see the same conversation on desktop and phone but now they work like two separate chat apps. I can't find away to link them back together. Any help appreciated.

I'm running latest OSX El Capitan 10.11.6 and iOS 9.3.4