Retopology invalidates shape keys?

I did a local retopology of a model, i.e. in an area that is not affected by any shapekeys. However, I found that now all shape keys give me extreme distortions throughout the whole model, so I have to redefine all of them. Am I overlooking something, or should I really stick to a strict workflow where modelling comes first, and modelling the shape keys come next, i.e. after retopology I have to redo my shape keys? That makes it impossible to do minor topology fixes, after the shape keys were done?