The movie was physically restored in 1997 THEN the new effects were created (you can't paste a shitty Jumanji dinosaur into an unrestored shot!) so all that stuff should be fine, i would think. And I don't think he would then throw out any original negative shots, if only because he might want them again for future changes.

I think 2009 is the ideal year to do a simple 3 disc Blu-ray set since...what else have they got to release for the year? And the sooner they do it the sooner they can double dip for the ultimate special versions, which is already the plan for Lord of the Rings and Star Trek. (basic theatricals now, more deluxe later). But that would be too normal.