You haven't provided your full code but it sounds like you have defined both aDoc and newDoc as the same document.
When your code starts up, you should define the activedocument before you start getting confused with a second document eg
Code:
Set aDoc = ActiveDocument
Then you can create and define the new document in a single line
Code:
Set newDoc = Documents.Add
This allows you to be very clear that these are two different documents, both open at the same time.