doubtful, if it did it would be in a backup directory in $mircdir
More likely, however, the files were just unloaded. Reload them, they should be in your last mirc directory.
Note that between 6.21 and 6.3 the default user data path changed from C:\Program Files\mIRC to you user's "Application Data" folder, or "AppData" under Vista. This does not affect upgraded versions assuming you installed over mIRC directly, but perhaps you installed it in another way.
