Unfortunately, we cannot recover data once it's lost.
If you noticed your save file is missing after booting up the game, do NOT continue playing. Instead, restart the game and see if your data pops again. You may have to restart the console as well.
If that does not work, start a new game and quit immediately during the first cutscene. Then select your file and choose LOAD GAME. If a BACKUP SAVE file containing your data appears, load this and create a manual save from this data.
Prior to a recent update, there was a bug that affected a small percentage of users who reported missing save files. This was addressed in update 1.002.000 and should not occur again. However, if your file was affected and has since disappeared, this isn't something we can recover.
If you have cloud saves via PlayStation Plus, it is worth checking to see if your data was backed up.