Seems like you need to backup your system via Time Machine or make a clone via Carbon Copy Cloner or SuperDuper onto an external HDD and erase the entire HDD via Disk Utility from the Restore DVD and restore from the Time Machine backup or clone the cloned backup back to the internal HDD.
It seems, Windows is gone. Do you have at least the lost GBs back, meaning if you have an HDD with a capacity of 500GB and used BCA to make a 100GB partition for Windows and had one partition for Mac OS X with 400GB and one partition for Windows with 100GB, do you have gained the 100GB back and now have a 500GB partition for Mac OS X again?