Using Action Replay is always a risk to mess up your save file. In this case, it appears that your AR has corrupted or even deleted the old data.
If the game does not recognize there is an old file, the chances of retrieving it are slim. You could perhaps see user reviews of the particular code you used, or do a Google search on retrieving game data.
As for the speculation about a virus, an AR code would only need to have an honest error to cause some data corruption - but the possibility of a malicious code is always present. If you did a search for Pokemon cheats, you would find many guides on supposed "cheats" that only instruct you to waste time, or in the worst cases, restart your game.
If you are only trying to get a female when breeding, I would recommend simply breeding more eggs (the minimum chance of getting a female for any species is 1/8) or using an RNG calculator
, which cannot damage your game data.
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