Its not quite that simple and like most things around EU regulations, it is complicated and it all depends on what aspect you are talking about. I don't know all the ins and outs, but if you are talking from a railway certification perspective then yes it would be a new build, but from an emissions standards viewpoint, I believe it would be a rebuild.
Where the GBRf 73/9s were concerned, my understanding is that they were classed as rebuilds from the railway certification point of view, as long as the frames were original. Emissions standards did not really come into that as they were putting brand new MTU engines in, which had to meet the latest criteria. However, move away from railway certification and EU emissions standards are not too interested in frames (or even what mode of transport they are) purely the power unit - which could be for use in a railway locomotive, ship, or even a static power plant in a factory.
GBRf used this latter point to obtain its final batch 66/7s, which were ordered after the emissions regulations changed. From memory (I'll stand corrected) but EMD had four engines on the ground in Europe that were delivered but never fitted to a loco - hence the power unit had been delivered to Europe and had touched the soil, therefore it was in the EU while the old emissions standards were in place. These four were then shipped back to the states and incorporated into the final batch of 66/7s to be built - Nos. 66773 to 66779. Of the seven, four were the EU power units, one was the power unit from 66734, that was written off in the derailment at Loch Trieg, and the other two power units came from accident damaged Euro66s, meaning that GBRf could order seven locos after the deadline for new build engines.
Where the 69s are concerned, there is regulation whereby rebuilt locos are only required to meet the regulations that were inforce at the time of the construction, which means a lot more can be done.
Fire regulations are similar for example, I once asked a very Senior Manager at Virgin Trains East Coast why the new Class 800s could not simply have the Mk4 interior, it worked, it had been proved and was better than the DfT had specified. I was told "the seats in the Mk4 do not meet the latest fire regulations and cannot be use in the IET, we can use them in the Mk4, because being refurbished, the seats and internal spec only has to meet the fire regulations that were in force when the vehicles were built!" I'll not get into the IET specs here, because that is a whole different ballgame thanks to the DfT!!!!