A feature on 1up that deals with the difficulties various developers have had with re-mastering old games revealed that Hijinx Studios, who developed Silent Hill HD Collection had a lot to deal with during the 2 years (!) they worked on the project.
Senior associate producer Tommy Hulett told 1up the following:
"Game re-mastering isn't a quick and easy process. That first God of War Collection came out and did really well, and I think a lot of companies saw it as a good way to make a quick buck off old stuff. If you want to make a definitive version of a game, expect a serious time commitment. It's been more than two years since we began the Silent Hill Collection project. That's how long it took to make Silent Hill 2 in the first place."
"We got all the source code that Konami had on file -- which it turns out wasn't the final release version of the games! D'oh!" says Huelett, "So during debug we didn't just have to deal with the expected 'porting' bugs, but also had to squash some bugs that the original team obviously removed prior to release, but we'd never seen before. A lot of assets such as textures and sound had to be taken out of the compiled game, and that brings with it a host of unique issues, especially taken on top of the tricky coding workarounds at play in the original games. We certainly had our hands full. I think at one point [Silent Hill 3 protagonist] Heather was blue."
Hopefully, game publishers are better prepared these days and archive the code properly...