Hi, I'd like to help you with your question.
It sounds like your granddaughter has somehow picked up your daughter's fear and distress and is reacting to it in her own way. Your daughter's fear is understandable with what she went through. And it is great she is getting counseling to help her. However, she most likely unintentionally transferred her fear to her daughter. Or your granddaughter has overheard your daughter talk about what happened to her and your granddaughter, being only 3 years old, would not know how to interpret what she heard only the feelings behind it. So she would interpret that she is not safe.
To address this, first have your daughter talk to her. Ask her what she is afraid of. See if she will tell her. Tell her to be gentle and get at her daughter's level when she does this. If she won't talk about it, that is ok. Let your daughter know to tell your grandchild that everything is ok. Explain that Mommy has had some things happen but everything is alright and she is getting help to deal with it. If she can, have your granddaughter's father there as well. It sounds like she is afraid of men so the more gentle reassurance she receives from both parents, the better.
Ask your daughter to consider having your granddaughter see a child therapist for an evaluation. Your granddaughter may be developing some fears and phobias and the sooner she can get help, the better. If her fears are left untreated she may have trouble as she grows.
You an also talk with her. Reassure her that all is well. Be honest and open with her, but also age appropriate. Tell her that she is taken care of and she has nothing to worry about because she has lots of caring adults in her life. If you do that enough times, she will begin to understand.
Let your granddaughter talk as much as she needs to. Once she feels more comfortable, she may be willing to let you know what is going on with her. If not, have her draw something about how she feels. Then go over the drawing with her, asking her what everything means. This may help her open up.
I hope this has helped you,