I usually take the pool for granted these days and ignore it, but after having accidentally deleted a few audio files irretrievably, I thought I would investigate the correct settings.
I went to prefs and entered the setting “Copy files to project folder” and was expecting a folder called Audio in my project folder.
I think I have identified the problem, it’s only on IMPORT that the files are saved. Any already in a project before making the setting are not saved. This means you cannot take a project which was saved without this setting (above) ticked ., merely save it, then think everything is in the Audio Folder - its not. Only newly imported Audio will show up. As I had not altered the project, there was no new audio.
In addition to using the Archive/Backup functionality built into Cubase (and discussed in this thread), I also recommend making full point-in-time backups on a scheduled cadence to prevent (accidental) file deletions from rippling through any other backup schemes you may have in place.
For example, I make a full (compressed) copy of all of my Cubase projects (with all of their audio files) every month, and stash that away on a NAS and an external USB drive. It’s saved my bacon several times, when “somehow” a file went missing, and I was able to go back to one of those older archives and dig it back up.