There's many ways that different Zip files can contain the exact same content. A change to the order in which files are stored is likely to be the primary one.

There's many ways that different Zip files can contain the exact same content. A change to the order in which files are stored is likely to be the primary one. Zip also has optional ZIP64 headers (required for large files) and a switch to using these would be another example. Assuming Github don't actually store the files (maybe they cache frequently used ones), sounds like you spotted the roll out of some new code. These sorts of issues come up when you're reliant on sorting a list of files -- because it depends on an idea of the alphabet, which comes from the locale in the environment you run in (could be "POSIX" or "en_GB"). Now you can see why a changes from outside the code could cause the unintended side effect you might be seeing here.