I bet the Flash won't be in the movie. WB tells the TV division who they can and can't use. I would think if there were immediate plans to put The Flash into a movie, they wouldn't be going forward with the TV show. I think they are conscious of audience confusion. (whether that's a concern they should be concerned about is a debate.)
The situation with the X-men movies and the Avengers using Quicksilver and the Scarlet Witch is a different one--selling rights to characters. While WB keeps it all in house for the most part.