I know I can "probably" fix them by using "flip -u" (cygwin flip) which basically removes one of the 0xd's leaving the file with DOS style line endings (0x0d 0x0a) (of course, technically speaking this might be considered a bug!).
But the other side of it is that i'd like to do this selectively, ensuring that what I'm fixing really is a "non-binary" file and EXPLICITLY replacing the 0x0d 0x0d 0x0a sequence with 0x0d 0x0a... not running a buggy program that appears to do what I want (and possibly more).
Note that grep -P '\x0d\x0d\x0a' and grep -P '\x0d\x0d' do not find these lines.
Although people say that grep -P 'x0d\x0a' is properly finding line endings, I'd have to surmise that something else is going on since it can't match the other patterns in a file with mixed line endings (0x0d 0x0d 0x0a).