if you at any point uninstalled steam or besiege before without taking a backup of your Saved Machines folder you've lost your machines (unless they're on steam workshop). If you haven't then I don't know what caused it, but you probably lost them either way. You can try checking your saved machines folder to see if it's truly empty, but if it's not there they're gone.
If you computer takes regular full back-ups, you can try reverting to a time when you think you might have had all your machines, then copy them.
On windows you can try this with either your saved machines folder, besiege_data folder or steamapps/common folder:
https://www.howtogeek.com/howto/111...sions-of-files-in-every-edition-of-windows-7/
on macOS you can use Time Machine with the same folders:
https://support.apple.com/kb/PH25540?locale=en_US
As for completed levels, you can just edit CompletedLevels.txt