Unlike most HD Collections and HD Remasters of games, Silent Hill HD Collection made a number of changes to the core game, including the following from Silent Hill 2:

• The street and sidewalks textures have been changed to look much cleaner.
• The video tape in one of the game's cutscenes is now bordered by a TV screen rather than showing up full-screen.
• The cutscenes are stretched horizontally to appear as widescreen.
• The distances on the sign at the beginning have been altered.

These changes are most likely made because the team was working with unfinished code and had to recreate much of the game.

While the player is given the option to toggle between the original and new voiceovers in Silent Hill 2 HD, the option for original voices in SH3 HD is nonexistent. This is because Heather's original voice actor could not be contacted in time before the game's release.

The team behind the remaster, Hijinx, were supplied with buggy and unfinished code by Konami in order to create the updated versions. Konami didn't store the original finished development code in a usable format, and as such the team were tasked with fixing the bugs from the code along with porting the titles to new formats. This took the team 2 years to complete - the same volume of time it took for Silent Hill 2 to be developed in the first place.