They ended Arrow without any cliffhangers, so it could easily start up next season in the middle of a new timeline. The heroes from LoT could go off with Hourman and be outside the timeline when it shifts, and so not affecting them.True. Supergirl didn't really fit into the CBS style of shows. CW is a better fit.
But again, another season finale and another reset button clicked by Barry. I didn't see a ripple effect in the season finale of Arrow, but maybe this happened after that show aired?
Not sure what they would do with Supergirl, though. That did end with a cliffhanger and looked to be heading in certain directions. I assume they wouldn't want to just throw that all away.