Hi acdkayakHL7:
It would seem to me that any updates that you are making to the map in your Visual Studio project are not being reflected at runtime after you redeploy the project containing your map. Did you check the properties of your project and make sure that the following settings are set up correctly under Configuration Properties -> Deployment:
1) Redeploy: True
2) Install to Global Assembly Cache: True
Also, you mention that “field mappings are being lost”: when you open your map in Visual Studio, does it prompt you to select a different schema for either (or both) source and destination? Make sure that you did not modify any schema(s) being used by this map (i.e. changing Target Namespace, fields or attributes), otherwise, you could lose some of the field mappings.
I hope this post resolves your issues.
Daniel.