I have had this sort of situation before, but not over a long period of time. I have a player who likes to go do her own thing, and I allow it, but I typically don't focus too much time and attention on her character while she's off doing that stuff.
For example, my players found these ancient ruins with the help of a wizened old scholar. Three of them decided to go exploring inside, while my snowflake player decided that she would stay outside to keep an eye on the scholar (since he was busy cataloging things and furiously taking notes about statues and such).
At that point, I spoke with her OOC and said something to the effect of: "You can certainly stay out here and watch this guy, but most of the action is going to happen inside the ruins. If you're ok with a minimal role over the next session or two, that's fine - but I want to make you aware of the consequence of these choices."
She was fine with this, and so the session progressed where I focused 80% of my attention on the players following the plot and 20% of the time on the player outside doing essentially nothing.
In your situation, you might do something similar. Warn your snowflake player that he can "go explore that empty alley" or whatever, but then spend the next large chunk of time focusing on the players sticking to the adventure.