Another user encountered the problem that if they saved all of their project files inside the AutoSave folder, Dorico would delete them, which is indeed exactly how auto-save is designed to work – the assumption is that any file in that folder was put there by Dorico, so it can safely delete it when the program quits cleanly. The reason we chose to expose the location of the auto-save folder was so that users could e.g. specify where it should be, but I confess that it never occurred to me that you would choose to start saving the files you wanted to keep inside this folder.
Consequently we have made a change ahead of the next major version that will remove the choice of where the AutoSave folder will be located, and it will be hidden away out of sight in the hopes that it will prevent you from inadvertently saving projects in that folder yourself.