As I had noted in another recent post on LabVIEW and .NET, the LabVIEW <-> .NET interface is not the most robust in the world. It has improved considerably over the LabVIEW versions. It also depends on whether you're dealing with a private assembly that's in a specific folder, or a strongly named assembly that's in the GAC.
I'm currently using 8.2, and version changes to assemblies are a sometimes real pain. I've never had to recreate a VI entirely, but sometimes I've had to delete the .NET controls/indicators and place new ones, or delete the constructor only and place a new one. Even them I've sometimes had to go and reselect the methods and/or properties.
I don't know how you have your code setup, but you may find the the following of some help:
How LabVIEW Locates .NET Assemblies