They used to and probably still do destroy their gold masters after a relatively short time for some reason, they do this with vidya as well as anime. Nips being nips.
Edit: As an example, because of this practice the brunt of the earliest episodes of Sazae-san, the longest running anime in history (starting in 1969, the manga in 19motherfucking46, over 7000 episodes), only exist on old VHS tapes in some otaku's basement Scratch that, VHS came out in 1976 in Japan, those episodes are lost media. I really have no idea what's the motive behind destroying the source of beloved media.
I know that in the case of Konami, the cause is usually hard drive failure. That doesn't make it acceptable, but does explain it happening out of negligence rather than malice.
I actually managed to flag down one of the devs behind Harmony of Despair (the fun/silly multiplayer one on XBOX 360 and PS3), and they essentially told me that the reason you're never going to see a "proper" release of Symphony of the Night (I.E. including all the new content the Saturn version had, the old Richter sprite with the tailcoat, the new animations for Alucard, the new castle zones, etc) is that they lost the files used for that shit back in like 2001 due to a massive computer failure. The devs behind Castlevania X Chronicles (the PSP port on which all HD versions of SOTN are now based) wanted to include all that shit to make
the definitive version of SOTN, but no one at Konami had the files and extracting the data manually would have taken like two years, because they would have had to do what Bluepoint does and reverse-engineer that shit.
In the end, the only extra they could add aside from the new script and redone castle layout was extract Maria and make her playable.
That shit is also why Harmony of Despair had such a troubled development. They wanted to include Trevor Belmont, Hammer, and like half a dozen other characters, but couldn't get the data extracted or completed in time. Voice barks actually exist for those characters in-game as well as responses by the other characters! Trevor was going to used a recolored Old Richter sprite, but they couldn't get it working. Hammer only had half a sprite-sheet in Dawn of Sorrow, one of the few games they had Archive data for, and there wasn't time to complete it from scratch. A lot of the things they wanted to do they couldn't because Konami lost the source files for basically all of them. The reason the last two maps before the retro stages were from SOTN is because the team behind CVXC held onto their work from porting Maria and basically handed it to the HOD devs going: "Uhhhh.... Here ya go."