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The Stratagem says:

"Use this Stratagem in your Command phase. Select one Black Legion Heretic Astartes unit from your army, then select one Legion Trait (pg 78 - 105). Until the start of your next Command phase, models in that unit have that Legion Trait. You can only use this Stratagem once."

My question is does the unit selected have both the Legion Trait of the Black Legion; Black Crusaders, as well as the selected legion trait, for example Profane Zeal or does it only have the new selected Legion Trait until the start of my next command phase?

The unit has both legion traits.

They have that trait, and nothing says they lose their original BL legion trait, so they have both.