Dock items sync with iPhone?

Hey guys,

I recently purchased a 128 GB MBP, and decided I needed the 256 GB, so I exchanged them and used Migration Assistant to transfer my data to the 256 GB via WiFi.

After transferring, I'm noticing that some icons on the dock are no longer coming up. I'll try my best to explain..

When I used to open iMessage on my MBP, and then open iMessage on my iPhone, another iMessage icon would pop up on the left side of my dock with a little phone symbol next to it to show I had it opened on my phone. Similar with notes and Safari. However after migrating this no longer occurs - I'm worried this might cause some sync issues between my phone and my computer - how can I fix this?