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I want to use an HA greninja competitively, but Im scared when I breed it it wont have its HA. I'm thinking if I save right before the egg hatches, I can just keep soft reseting. but I'm scared that the game doesn't code the probability of the HA being there when you have the egg. when does the coding add the HA, and when should I save?

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All the values relating to the baby Pokemon are decided when the egg is created, when you accept the egg from the Daycare Helper. Nature, IVs, Egg Moves, Ability, everything. Saving after this point will not help in anyway, you must save before it. For this reason, soft-resetting is not an effective method for your purposes.

As for passing HAs, one of the parents must already have the HA for the babies to inherit. If breeding with different species, this means the mother is required to have the HA, as the mother determines which specie. The mother has an 80% chance to pass down HA, the father when same specie has a 20% chance to pass down HA.

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Actually, it's even sooner than that. As soon as you accept (or reject) an egg, all the values for the NEXT egg are set. This is a known method for getting 5-6 perfect IV's, as you can rearrange the parents with this information in hand. PhailRaptor is correct in saying this is not an effective method, as it would mean hatching single eggs to check them. Just keep breeding until you get a Protean Froakie, there is no real method to it. The method you're proposing is more suited to IV breeding..
that's only in sun/moon though, which is how shiny swapping works. I wish I had seen this befoe spending 20 inutes soft-resetting that masuda-drilbur egg....
nope, as far back as X/Y. Trust me, I've been using it on those games
you've been shiny swapping in X/Y?
i feel old
Wait, if you breed with Ditto, will it still pass down the ability? I've tried three times already, but no success...
@noaisawsom123 If the Ditto is replacing the mother, and the father has their HA, there is a 20% chance.  If the Ditto is replacing the father, and the mother has their HA, there is an 80% chance.
@PhailRaptor Ok, thanks. I had a HA Gardevoir that I wanted to breed, and I attempted three times with no success.