I think I can help in part. Others please feel free to join, (and if someone has a ready answer to waftlord’s question, skip this post).
Based on what I have read so far, samples may be put in any folder structure, and even their names do not count because what is used for reference is a unique “checksum” of files.
Sounds saved on +Drive are for user to draw from when needed, i.e. not directly relevant to project recovery.
Patterns which don’t use sound triggers do not rely on sound pools at all (0 position Track sound in sound pool).
For patterns which use sound triggers, sound pools are used and the sound pool is position dependant and unique to the whole project.
You can’t save a sound pool on +drive as part of Rytm operation but you can use sysex dumps (i.e. not handled separately by Transfer)
When a recovered project is playing stuff, it might be either due to sound pool or to sample association having been messed up.
Experienced Rytm users, is this correct? How to address the issues mentioned above?