IMHO, that's a wee bit more than a scratch.
Looking at that while putting in on my wrist would make me sick. 
I know I would replace the case for cosmetic reasons alone. Now to the length of time between the hit to the case and the subsequent problems with the chrono. The operating levers for the chrono are, by necessity, close to the case wall because of the proximity to the pushers. The operating levers are held in place by screws and springs to keep them from conflicting with each other.
The impact could have loosened a screw that, after a while, backed out by the motion of the lever to the point that it allowed the lever to go where it is not supposed to be. Or, a spring could have come loose and the chrono kept working until the case was in a certain plane that permitted unwanted interference when the pusher was activated. This is all conjecture on my part because I haven't seen the watch. Having worked on a few, I know there is usually not a lot of clearance for things to operate properly and even the slightest misalignment can cause major problems.
Good luck with the repair.