Im just now into the beginning of act 2 and shes already 100%. I had the scene at the estate. and after i chose "Why Not?" but forgot to investigate all three options. Does this mean i cant complete it and get the trophy or will i be ok? --- Let's get it on FREAK!!
If you asked "Why not?" and do not pursue any other romance (turn away Merrill if she shows up) and (obviously!) do not turn her over to the Arishok at the end of the act, your romance should remain active and, when you do her act 3 personal quest Isabela will confess her love. (She never moves in, though.)
She should have a wardrobe change (to the black corset with armband) which is sort of bugged when she has been romanced. Going to the Black Emporium with her usually fixes this. --- We're having a great time: food, wine, a little personal abuse, and the universe going foom.