So a lot of people on here don't understand how the relationship between the DC movies and the DC TV shows work. I will try to explain it the best i can.
The thing that confuses most is how Deadshot has to die because of the movies, (along with Captain Boomerang) but Superman and the Flash still can stay around. In order to explain how that works, i'll be spoiling major plotlines from the shows and the DC movies.
I'll begin with Deadshot because that is how this all started. Suicide Squad was in production around his death. So DC wanted to make sure that the TV Suicide Squad was over so that it wouldn't be confusing. That and they didn't want the shows to upstage them. He died in Suicidal Tendencies. However this is when things get tricky, he eventually came back. In season 5, Deadshot came back as a hallucination for Diggle. This was allowed because Suicide Squad was released already and there was no issue about TV's Deadshot upstaging Will because of the fact that there was no Suicide Squad movie currently in theaters.
Another tricky character to get around is Superman. This guy is as iconic as they come so naturally he has tons of films about him. However the TV world didn't have access to him for Supergirl's first season because of Batman v Superman: Dawn of Justice. The thing is that in this movie, Superman died in order to inspire the formation of the Justice League. So now the shows were allowed to use Superman for the second season due to his lack of use in the movies. He appeared four times, however he once again went back to Metropolis by the time of the finale because of Justice League being released soon.
The final one is the Flash. This is the one people have pondered the most about because he has made a whole bunch of cameo appearances in the movies now. Suicide Squad, BvS, they have both used him. However one of the shows star the Flash, so why is it still on? Well i'll tell you. So far the Flash has only made small appearances in these movies. Barely enough for DC to fear the show is going to be compared to this version of the character. However Justice League is closely coming up and that means that the Flash has to go... to the Speed Force. This happened in the Flash season finale. Allowing Wally West to take up the mantle so there isn't two Barry's by the time of Justice League and Flash season 4.
I hope my explanation has cleared things up for those who didn't understand how this worked. If not, comment about your questions.