SilverWook said:

Time and technology marches on. One one of the ROTS commentaries, there is mention of some doubt at ILM that they could plug in the Episode One model of Boss Nass into the software they were using at the time. That's only about a six year span.

Data files can get lost or even wiped. Just ask Pixar. ;)

Doesn't seem like there would be a lot of point to save the effect files, except just to have them. Since AOTC and ROTS have a good amount of effects shots, I'm guessing a lot of hard drive would be required to hold all the files. It's been said Lucas has copies of everything, so I wouldn't be surprised if the effects files were housed somewhere.