I do not want to include the sounds IN the AUP file… I have just left the sound file beside; but I changed the name of the main file including eithe the projects and the sounds…
Delete the parts that you have destroyed (the bits with no sound), then import the files back in again.
See here for how to safely handle projects, particularly the part about “dependencies”: http://manual.audacityteam.org/o/man/audacity_projects.html