Lets say i have a Baratheon deck in which i have different copies of Shireen Baratheon.

Shireen Baratheon comes into play and subsequently becomes my character agenda .

I then play the other version of Shireen Baratheon. Does this Shireen adopt the text of the previous, and now agenda Shireen, or would it retain its own text based on the fact that the 1st Shireen is now an agenda ?

I hope this makes sense.

Thanks

The card keeps its own text (just as it would if Shireen had been discarded from play before you played the new version). The only way in which its text would "change" is if it were played as a duplicate on the other Shireen (who would have to be in play).