I did the same thing. Did my home state full-year resident with earned income in another state, and did a part-year non-resident GA form. Turbotax does a good job helping you select which forms to file.

The gist is that your 'training pay' is income earned and taxable in GA, and once you converted to 'flight pay' (post IOE) it is income earned and taxable in your tax home state.

It's not double taxed because each state asks if you had any income earned in another state and then excludes that income from its calculations.

You should be able to designate how much of your annual income was attributed to each state, indicate how much tax was withheld from each state and your refund/bill should be calculated separately.

The kicker for me is that I had to file GA for two years since I started training late in one year and didn't complete IOE until mid-January the NEXT year. I earned a couple hundred bucks attributed to GA income the second year, but still had to file. What a PITA!!!!