The route is still being served non-stop in June on Mondays and Fridays (with some flights on Wednesdays early in the month). Some other days of the week there are semi-reasonable connecting initeraries available, too. There are also flights to Austin from Atlanta on other days of the week. So you could probably make something work if you wanted to.

F9 has frequent schedule changes, particularly if you book more than a month or so in advance. The airline industry is desperately trying to balance supply with demand right now so it may be more pronounced than normal.