As you all surely know, when someone gets a Gift of the Gods, if they are aligned, most of them have extra effects depending on your alignment.

Fair enough. You get Slayer Limb and you're Aligned to Tzeentch, the weapon gets the Warp Weapon Quality.

However, what if you are Unaligned and is Aligned at a later point? Does the effects apply retroactively? If you get Slayer Limb when Unaligned, and then become Aligned to Tzeentch, does the weapon gain the Warp Weapon Quality?

As far as I know, the gifts remain "as is" when you receive them, unless something forces the gift to change (like that Tzeentch-specific reward).

^this

There's sadly no specific mention of what happens. I could see it be interpreted/ruled both ways. On one hand, you have static 'what you get you keep' and then you considering the everchanging nature of chaos, and it's not so hard to imagine gifts evolving/changing/shifting with your alignment to the gods.

Personally I'd probably rule it that a gift received as a reward updates itself and a gift received as a punishment for failings doesn't. Houserules, obviously, but I think well within the realm of GM Discretion.

There's also that one gift that becomes less powerful if you're aligned, Magnificent Horns I think it's called. Not very powerful or anything, but just something to keep in mind for consistency's sake whichever way you go with it.

I do not believe that they should change. It is if anything a punishment from your god to not have aligned with them sooner to receive their boon. Why would a god be benevolent enough to go back and help you amend your gifts granted from lesser beings to allow them to benefit from their own blessings?

Well, depending on whether or not they have plans for you. Why would they give you any other gifts such as a daemon weapon?

I think a case could be made for either option. On the one hand, it could represent the entirety of the Heretic's body being brought that much closer to the entity that is now going to claim their soul once it is time. On the other, they could simply ignore existing mutations just like they ignore the normal condition of the body, limiting any changes to those that are subsequently rolled on the table.