that is for time played, when you save in game it shows PLAYER, BADGES, POKéDEX, TIME. its that time. if you want to adjust your ingame clock. reset the RTC load game on cart and save, then edit the initial RTC value, I think for every hour you move to value back, an extra hour passes ingame.
I think I will leave it like that, or maybe have them show up as bad eggs? they are perfectly fine Pokemon data, its just the Pokemon id are set to 0 for some reason, so they are not shown in-game. where they there before and disappeared after using my program? or you had no idea they where there? maybe they got changed from AR codes or something along time ago. do you have any backups of the save that was never edited?