Could you use pointers? I know on psp rips I made back in the day where the memory sticks where extremly small you'd just point to smaller files. Example there was a dirt game where the game had different engine sounds for all the cars. I found the smallest sound sample and just made every car only use that sound and removed all the rest of them. Saved a huge amount of room.It's because the Neo Geo CD system only has 1 megabyte of ram for V rom data (sound samples). For most games to fit, you have to trim the game's V rom data to be smaller than 1 megabyte.
Then when the game needs to access any of that sample data that got trimmed off, your speakers get filled with that glitchy mess instead of the intended sound.
The way to fix this would be to program load screens in the middle of the game, but that's too much effort. That's why most conversions are only for the smaller games, that fit within the Neo Geo CD's ram limitations.