Eurocopter does indeed deliver apparently "new" aircraft with some used parts or components fitted. The component history section of the log book will show exactly what and where. They are purchased as re-manufactured aircraft and priced accordingly.
These aircraft generally have a S/N range that differs from the main production range. An example is the re-manufactured AS 350 series aircraft that are delivered with S/N's in the 9000 range whereas the production 350's start at S/N 1000 with new deliveries currently up around S/N 4000+.
Not all parts delivered are "new" either. A quick look at Block 12 on the Form 1 will show the condition. If the part is obviously not in the condition stated in Block 12, you possibly have a bogus part on your hands.
The notion of "Have also seen refurbed 365 parts in factory packing from EC as new parts......" needs some clarification. Was it that the parts were in new packaging or did they differ from the Form 1 statement? Did the Form 1 state "New"? Was any action taken?