My guess is that checking code can be very complicated. In large companies development of computer programming code develops over long periods of time. To keep track of the development and history of their code companies use version control programs. This is necessary because as software code is developed there can be variations to subsets of it for testing purposes or parallel development of related features, etc. Version control systems can be very complicated.
If VHC is granted access to Apple's code, it is essentially 100% certain that a Special Master would be the intermediate agent to examine the code. My guess is that the court would require Apple to certify that what the Special Master is given access to is the actual Apple code repository. Most likely it would be a small portion of the Apple code since my guess is that Apple does not keep all their code in one place.
Also, there are two issues that should be clarified. There are two areas to think about. The code itself (also called "source code") and the documentation of the code.
The code consists of the computer program instructions that tell the computer what to do. Programmers can read the source code and understand the process intended by the programmer. Since VHC has patents on processes, not particular code implementations of those processes, a non-Apple programmer could look at relevent code and determine if the processes symbolized in the code parallel VHC processes.
The documentation helps explain for human readers various details about the processes of the code, along with supplemental information that is helpful for coordinating with other programmers. The documentation is used for more than that, but that is the basic idea.
I have written code and placed information in the documentation about where I got some portions of code, or where the idea came from. Including this type of information in the documentation can help other programmers understand what I was trying to do, or go to those other information sources to get additional information.
Who knows if Apple places that kind of information in their documentation. But the key point I want to make is that a qualified Special Master should be able to determine if the processes in Apple's code are essentially the same as VHC's patented processes with or without documentation that says "this was stolen from VHC"