N., Sarah is dead-on with her suggestion to consider some kind of computer linked sommunication system whereby you can hook up a video camera and the kids can actually visit with each other online.
Karen is also right in saying it is actually a good thing your toddler is so bonded to her brother. Yes, it is sad to see how much she misses him and, hopefully, he misses her, too. Unfortunately, this is one of the lessons all children need to learn in life. Too many problems today are caused by children having no coping mechanism and not knowing how to deal with disappointments (and that's when they go into school with guns and shoot the place up!). How your children develop in this regard depends a lot on how and what you teach them in the way of coping skills. Try to help your daughter understand, on her level, that her bubby will be back to see her sometimes but will not be with her all the time anymore. Let her know that you, too, are sad that they cannot see Bubby as often but you all still love him and he loves you, too.
Help her to make cards and drawings and other little gifts for him and let her put them in the mail herself. This will help her to feel more connected to him.
If you do not have a warm relationship with the ex, work on thawing her out. Try to get her to understand this is not about her or you or your husband but about the kids. Point out that you know she loves her son more than anyone else could and you know she wants to do what is best for him ... and that includes keeping him in touch with the rest of his family.
Setting up a good computer camera system can be a little pricey and Bubby's mom may balk at shelling out for the added expense. You and your husband might have to pay double and supply her hardware as well as your own but, if you can afford it, it is well worth the expense.
As time goes on, she will likely ask about his less often but, whenever she talks to him or sees him (either on-camera or in person) she will go through a period of mourning for him again. Let her be your guide as to how to deal with her maturation process where her brother (and everything else) is concerned.
This is a life lesson that will help her deal with teenaged broken hearts and other adolescent trauma so don't let it upset you too much.