When I work with maya Mb files in Unity, the file gets converted into a prefab which becomes a problem when I apply any scripts or dynamics in unity to the prefab. If I make any adjustments in maya the prefab gets updated fine, however when i;ve made any changes in unity to the file, the prefab stops updating when I make adjustments in maya?
You will need to re-drag the prefab into your scene. You can't make changes to the Maya file in Unity and expect the Maya source file to update accordingly. It just doesn't work that way.
I was trying this today...you can make changes to animations in Maya and they will update your prefab with no problems. However, if you add any new geometry to the Maya scene, it will not update in Unity. You would have to re-drag your prefab back onto the Unity scene in order to access the new geometry version.
I hope this helps. Please let me know if you have any more questions.