I think you did not back up your projects correctly. Sorry :(
Also,
re-installing Sonar will never ever ever affect any of the projects stored on your PC.
First things first,did you delete your cakewalk projects?
Where did you back them up to?
Did you check your back ups before deleting the original projects?
Did you back them up in CWP and per project or CWB formats?
For your plugins, just scan the folder that the dll's are in. Its called the VST scan.
Cj