Ask Preston Garvey and the Minutemen. Probably she has been kidnapped by some bandits.
As a Whiterun inhabitant (and that's not changed by your adopting her, although it should be) she goes into hiding when the Whiterun siege starts. You probably have to advance the Civil War quest line to have her re-appear. USLEEP/USSEP may fix this, but I don't often do the CW, so I'm not sure.
Don't worry, she's just playing safe!
Maybe she ran away?
Use the console to move her back to you.
I think she just disappeared due to the quest you are on. Move along with the Civil War business and she should return. Also make sure you don't have any mods like 'Immersive Citizens' or the like going because I had NPCs disappear on me left and right with that mod.