I think I have a way of dealing with that. It does that random file naming thing to be able to have past versions and then uses an internal database to keep track of which file is at what path and which version.
So a bit complicated... but for a reason.
I think I'll be able to have backups of the files in the places that you expect them to be with folder and file names.
That way, I can export to to another solution or restore if the main server goes down and needs to be rebuilt (but I'll have backup of that, too).