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Unfortunately your detective work on the Frontier site is correct -- service to Flint is being discontinued in early March. Fiint's service on Frontier is out of the Milwaukee hub with regional jets. As the Milwaukee hub is being downsized and regional jets are being parked, Flint's service is ending.
The other complicating factor is that Frontier's schedule isn't quite available for fall purchase yet. Same goes for a few other airlines, including Southwest and AirTran. The "legacy" airlines like Delta, United and American usually put their schedule up for sale nearly a year in advance, but many of the newer airlines only have a window of 6-8 months.
Frontier still serves Detroit and Grand Rapids, and with flights to Denver you can get to San Diego with a single plane change there. Grand Rapids isn't so bad if you're more west, like Howell or Lansing, but it's a long treck if you're someplace like Port Huron or Mt Clemens.