The company tells us NOT to flex on a contaminated runway or when windshear is expected. I add onto that when it's foggy and low visibility procedures are in force or when the runway is of a very bad quality with a lot of bumps and ridges: it is not wise or comfortable to use flex in those circumstances.
But all in all, I use flex as prescribed by the company in 99% of my departures.
I uplink the route data on almost every flight, unless there is no comms coverage. This saves me entering the wind data waypoint by waypoint. However performance is calculated on board in my outfit.