Im Wondering If I Copy some of my backup copies of my games on to my HDD when flashed my drive back to stock firmware could I play games online off of my HDD????
Unless you are a Pirate, the answer is Yes.
The Xbox 360 will allow you to install the games on the hard drive, but the disc is required in the drive.
Since you are copying a "Backup" as you say, you can flash back to stock, then put your ORIGINAL copy in the drive and it will read it off the Hard drive.