I doubt they saved the digital files because for the 2004/11 SE it looks like they either painted over the existing work or went back to the original pre-comp camera negatives (e.g., this is what it looks like they did for the re-done Jabba).

They probably did save some elements though--a lot of them were re-used in TPM. The one exception to my theory that I can see is that they re-did the "entering Mos Eisley" shot and completely re-comped individual elements--so maybe there was some instances where they had all the digital data for the scene. It's really impossible to say what they have and don't have because it's all just files sitting on a computer that only select ILM employees even know about. But it certainly seems like there is no massive "1997 Special Edition" server that has every scene, element, plate and work record.

And yeah, the 1997 shots are from film scans, not a direct-digital transfer. It's the 1997 film-out that was cut into the negative. This is part of what makes me think a lot of the raw data is gone, or at least the whole scenes. Probably a lot of the data can't be read very easily now anyway, the systems they built and rendered them on aren't used any more and you'd have to probably convert them into a readible format or write a lot of custom software to get the new programs to read and run it.