[cduan]

I think that they mean copyright registrations, not patent applications:

http://www.copyright.gov/eco/help-deposit.html

"In any copy option where portions of the code are blocked out, the blocked-out portions must be proportionately less than the material remaining."

Though most people I know just use the option to submit object code, since (1) the object code is usually available anyway to anyone who buys the software and (2) since you only have to submit about 50 pages of object code, you're not giving much away anyway.