If it has been more than 90 days since my initial counseling and flag (APFT failure), is there anything I can do if I can't pass a retake?

Physical fitness is a personal responsibility, conducting training and paternity leave will be no excuse for failing a pt test. The fact you cany do a measly 42, 56, and some abysmal 2 mile time should make you reconsider career options.
However, the good news is that legal will probably throw the packet back and the flags will be dropped. Until they administer another apft because you are still missing a current score for DTMS, then they will restart the process and you will back where you started.

PT like your gear readiness is your responsibility. You can't blame the unit for training, nor the baby. It is your problem to fix. They gave you a flag as a warning to get moving, and evidently you ignored it. Fail this next time and you could end up back as a civilian, looking for work.They have given you 90 days to get ready and you did not use it- and it will be doubtful if you can fight it, if you manage to win, it will only be temporary as you seem to ignore the warnings.

this basic question has been posed in a variety of ways over the past few weeks. basically, you can be tested at any point, no warning. it is your responsibility to be ready for the test SFC (Join to see) LTC Stephen F. LTC Jeff Shearer