Scott
Just copy the generated code for a field (BO.designer.cs or BO.designer.vb  and go back into the BO Mapper. Selec the field in question and then click "Custom Code." Paste the copied field property into the text box at the bottom. Change the name in brackets to a different name but leave the name that is returned alone.
Example:
Public Property [ChangeThisValue] As String
This way when you rebuild your partials it will not overwrite your changes. This way you can just change the name of the field while still referencing the old field name internally.