"Color film copy transparency" means the archive first made a photographic copy of the item onto color film, then produced a positive transparency (slide) from that copy, and finally scanned that transparency to create the digital image. In other words, the digital file comes from an intermediate film copy, not directly from the original object.

"Digital file from original" means the original item itself was digitized, either by scanning it directly or photographing it with a digital camera.

So the key difference is the source used for digitization: a film-based copy versus the original item itself.