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I generated a patch with the diff tool and when I'd apply it with patch-ng (through conan originally) it would confusing delete all the changed files. It turns out it was due to the line below which overwrites the output path (and ignores the patch) on files with bad dates. The mac os patch tool did not exhibit this behavior and it seems like at the very least it should be an error (since there is a change to the file, and an output path).
if (date == b'1970-01-01' or date == b'1969-12-31') and time.split(b':',1)[1] == b'00:00': srcname = b'/dev/null'
Note, the files with the bad dates which caused the diff tool to generate bad dates in the patch were from a conan export-source .tgz (not sure if this is relevant).