Most likely transplant shock. You don't say where you are located but separating plants in basket now that have grown together since early spring is generally a recipe for some major shock and root disruption. That combined with any weather issues can certainly create stress and cause the symptoms you describe. Just keep the plants well but not over watered. They should recover.

Absolutely transplant shock. I would strongly recommend pinching off the existing blooms, so the plants energy goes back into recovering.

I'd hazard a guess that the plant bought was a young one...possibly grown that year in a greenhouse and its roots are not all that strong. Then you separated them --possibly you did this opation in the sunlight---and the plant went into shock. Any plant so divided in daylight without first being given water--might act the same way.

All you can do is make sure the roots are established in soil that drains well. Many window boxes do not drain well--they harbor wet and when you watered, then it rained, well there's not much to say for the poor roots.

They'll come back---geraniums are pretty tough, but don't drown them and make sure the container they're in drains well.
Don't fertilize them into submission...let them get going first, produce new leaves, before feeding them.