Atmosphere's LayeredFS only requires the new files to mod the original files. There's no need to dump the collection.This is still unclear to me. In your first post it says to dump?
cue + bin files (and ini, if you want to active widescreen and 4MB) are the bare minimum required to swap games.
So:
- Get the game you want to replace in cue + bin or cue + bins format.
- Rename the cue to Cotton2.cue, don't touch the bin file/s.
- Move all files to atmosphere/contents/0100094014BE4006/romfs
- Launch the collection and play Cotton 2.