That's what happens when you mess with a past timeline; the present timeline is likely to be changed. He waited too long to realize and fix his mistake. It was too late to change the present timeline back in order. Barry will have to live with the consequences of his decision to mess with time and work to mend Joe and Iris' relationship the old fashioned way. I'm glad he didn't get to 'fix' it all nice and tidy. That's not how it is supposed to work!