It was hard for them.
Trying to adjust back to how their life had been before the Fall. Before the lie separated them to different sides of the world as Sherlock fought and fought every day and John remained stuck in a life seemingly lacking in the great man that had been- was his best friend.
It made John sick sometimes to glance over at the man with his dark curls and pale neck and remember that not all too long ago, he had been thought of as dead. For three years.
The longest three years of John's life.
It was hard for him especially because he found it hard to trust Sherlock as deeply as he once had. How was he supposed to know if the man sitting next to him one minute would be up and gone the next without a word?
The trust was there, as it always would be, but it was weak. Weak and fragile and something they never spoke aloud of. Much like the moments when Sherlock would slip his hand into John's, intertwining their mismatched fingers. Long, ivory fingers and short, calloused ones silently holding onto each other for the dear life.
There was a lot that they didn't speak about since Sherlock returned from the "dead", but that was all okay.
These things just took time.