Hi,
On the iPhone > Settings > Messages > Send and Receive is the iPhone number ticked (it is always greyed out)
Although being greyed out means the user cannot change this and it should always be Logged in I have seen it twice on Mine when it was not.
I had to Sign Out of the Apple ID then turn Messages Off in Settings and wait.
Then after a short period turn Messages Back on and wait for the Number to Verify.
I then tested from the iPhone by addressing the Apple ID specifically (Direct to my Mac effectively) before adding back the Apple ID to link and sync them again.
You will unfortunately lose any iMessages you have missed as they are not kept and the iPhone number was effectively de-registered.
7:34 pm Thursday; December 24, 2015
iMac 2.5Ghz i5 2011 (Mavericks 10.9)
G4/1GhzDual MDD (Leopard 10.5.8)
MacBookPro 2Gb (Snow Leopard 10.6.8)
Mac OS X (10.6.8),
Couple of iPhones and an iPad