I remember reading that Bluepoint for their several HD collections reverse engineered the code from the retail discs. With that in mind it's baffling that Konami/Hijinx would not do the same when they didn't have a finished code version on record.
The link to 1up is not working but I have the text from a interview with tomm hulett on the problem with preservation.
The lesson then would seem to be that if better archiving were done in the past, we would have better re-masters today. "Ten years ago, a lot of game companies assumed the games were 'done' once development finished, and that they wouldn't need to use that data ever again. Now it's clear that having all that data in an easy-to-manage format is important. Many consumers don't realize you can't just buy a copy of SH2 and then open up its code in a usable state."
It may not been in a usable state, but they can most certainly use that retail disc for making a high quality re-master. Huelett's team at Konami and Egan's team at Sanzaru were both working from source code provided by either the publisher or the studio that originally made the games they were in charge of re-mastering, while O'Neil's team at Bluepoint went back to Santa Monica only for certain assets. Using legacy code is not always be the best way to create the best possible HD re-master. Bluepoint's track record with God of War, Metal Gear, and Team Ico's game shows that their method might be preferable: Don't use old code, use the finished game itself.