I am not sure what you have done, but gc is called "Garbage collection".. It only gets rid of commits and the objects related to those commits (eg git backup files) that are no longer being referenced by tags/branches/heads.
This does not touch the working tree (eg, the files you are currently working on). Only unneeded commits from the past.
I am not sure what you had done, but I have never seen SmartGit cleanup do anything close to the destruction you are mentioning.