When I drag a tunnel (to flip the line e.g. from straight-diagonal to diagonal-straight), the tunnel count sometimes changes +/-1. I’ve been able to make it flip between 1 and 2 by just dragging my tunnels, and it happens even if they go back to the same location after letting go. I’ve never been able to shift the count more than one step.
Possibly related, I tried to drag the line between two stations on the same shore of a river bend. When I had the line over water, the tunnel count decreased by 2 instead of 1. It did however change back +2 when I let go and the line flipped back to be on ground.
This is on the Paris map. Steam Linux, version 201612231225 (gamma15). I can upload the savegame somewhere if it’s useful.